On EU/EEA applications under freedom of movement: see page 82: PART III:SPECIFIC RULES RELATINGTO APPLICANTS WHO ARE FAMILYMEMBERS OF EU CITIZENSOR SWISS CITIZENS

A few pages onward is a summary that further explains the direcitve and application form:
(....)

3.
SPECIFIC DEROGATIONS FROM THE GENERAL RULES OF THE VISA CODE

This point provides for operational instructions concerning the specific derogations from the general rules of the Visa Code that are to be applied when it has
been ascertained that the visa applicant falls under the Directive and that there is no exemption from the visa requirement.

3.1.
Visa Fee

No visa fee can be charged.

3.2.
Service fee in case of outsourcing

of the collection of applications As family members should not pay any fee when submitting the application, they cannot be
obliged to obtain an appointment via a premium call line or via an external provider whose services are charged to the applicant. Fam
ily members must be allowed to lodge their application directly at the consulate without any costs. However, if family members decide
not to make use of their right to lodge their application directly at the consulate but to use the extra services, they should pay for these services.
If an appointment system is nevert heless in place, separate call lines (at ordinary local tariff) to the consulate should be put at the dispos
al of family members respecting comparable standards to those of "premium lines", i.e. the availability of such lines should be of standards
comparable to those in place for other categories of applicants and an appointment must be allocated without delay.

3.3.
Granting every facility

Member States shall grant third country family members of EU citizens falling under the Directive every facility to obtain the necessary visa. This notion must be interpreted as ensuring that Member States take all appropriate measures to ensure fulfilment of the obligations arising out of the right of free move ment and afford to such visa applicants the
best conditions to obtain the entry visa.

3.4.
Processing time

The visas must be issued as soon as possible and on the basis of an accelerated procedure and the procedures put in place by Member States
(with or without outsourcing) must allow to distinguish between the rights of a third country national who is a family member of an EU
citizen and other third country nationals. The former must be treated more favourably than the latter. Processing times for a visa application lodged
by a third-country national who is a family member of an EU citizen covered by the Directive going beyond 15 days should be exceptional and duly justified.

3.5.
Types of visa issued

Article 5(2) of the Directive provides that third-country nationals who are family members of EU citizens may only be required to have an entry visa in accordance with Regulation (EC)
No 539/2001.

3.6.
Supporting documents

In order to prove that the applicant has the right to be issued with an entry visa under the Directive, he must establish that he is a beneficiary of the Directive. This is done by
presenting documents relevant for the purposes of the three questions referred to above, i.e. proving that:
• there is an EU citizen from whom the visa applicant can derive any rights;
• the visa applicant is a family member (e.g. a marriage certificate, birth certificate,proof of dependency, serious health grounds, durability of partnerships ...) and his identity (passport); and
• the visa applicant accompanies or joins an EU citizen (e.g. a proof that the EU citizen already resides in the host Member State or a confirmation that the EU citizen will travel to
the host Member State).

It is an established principle of EU law in the area of free movement that visa applicants have the right of choice of the documentary evidence by which they wish to prove that they are
covered by the Directive (i.e. of the family link, dependency ...) . Member States may, however, ask for specific documents (e.g. a marriage certificate as the means of proving the
existence of marriage), but should not refuse other means of proof. For further information in relation to the documentation, see Commission Communication COM (2009) 313 final
22
.
3.7.
Burden of proof

The burden of proof applicable in the framework of the visa application under the Directive is twofold:
Firstly, it is up to the visa applicant to prove that he is a beneficiary of the Directive. He must be able to provide documentary evidence foreseen above as he must be able to present
evidence to support his claim. If he fails to provide such evidence, the consulate can conclude that the applicant is not entitled to the specific treatment under the Directive.

Additional documents may not be required regarding the purpose of travel and means of subsistence (e.g. proof of accommodation, proof of cost of travelling), which is reflected in
the exemption for family members of EU citizens from filling in the following fields of the visa application form:
Field 19: "current occupation";
Field 20 :"employer and employer's address and telephone number. For students, name and address of educational establishment";
Field 31: "surname and first name of the inviting person(s) in the Member State(s). If not applicable, name of hotel(s) or temporary a
ccommodation(s) in the Member State(s);
Field 32: "Name and address of inviting company/organisation";
Field 33: "Cost of travelling and living during the applicant's stay".

A Member State may require that the relevant documents are translated, notarised or legalised where the original document is drawn up in a language that is not understood by the
authorities of the Member State concerned or if there are doubts as to the authenticity of the document.

3.8.
Refusal to issue a visa

A family member may be refused a visa exclusively on the following grounds:
• the visa applicant failed to demonstrate that he is covered by the Directive on the basis of the visa application and attached supporting documents under point 3.6
(i.e. it is clear that the reply to at least one of the three questions referred to above is negative);
• the national authorities demonstrate that the visa applicant is a genuine, present and sufficiently serious threat to public policy, public security or public health; or
• the national authorities demonstrate that there was abuse or fraud.

In the latter two cases, the burden of proof lies with the national authorities as they must be able to present evidence to support their claim that the visa applicant
(who has presented sufficient evidence to attest that he/she meets the criteria in the Directive) should not be issued with an entry visa on grounds of public
policy, public security or public health or on grounds of abuse or fraud. The authorities must be able to build a convincing case while respecting all the safeguards of
the Directive which must be correctly and fully transposed in national law. The decision refusing the visa application on grounds of public policy, public security or public health or
on grounds of abuse or fraud must be notified in writing, fully justified (e.g. by listing all legal and material aspect taken into account when concluding that the
marriage is a marriage of convenience or that the presented birth certificate is fake) and must specify where and when the appeal can be lodged.

The refusal to issue an entry visa under the conditions of the Directive must be notified in writing, fully justified (e.g. by referring to the missing evidence), and sp
ecify where and when an appeal can be lodged.
A visa may not be refused on the sole ground that the applicant is a person for whom an alert has been entered into the SIS for the purpose of refusing entry into the territory of the
Member States. . Before refusing to issue a visa where there is an alert in the SIS, in any event it must be verified whether the person concerned represents a genuine, present
and sufficiently serious threat to public policy, and public security. For further information, see Commission Communication COM (2009) 313 final 24
.
3.9.
Notification and motivation of a refusal

Article 30 of the Directive provides that family members must be notified in writing of the refusal. Irrespective of the mandatory notification and motivation of refusals as provided by
the Visa Code (applicable from 5 April 2011) , refusal to issue a visa to a family member of an EU citizen must always be fully reasoned and list all the specific f
actual and legal grounds on which the negative decision was taken, so that the person concerned may take effective steps to ensure his defence
.
The refusal must also specify the court or administrative authority with which the person concerned may lodge an appeal and the time limit for the appeal. Forms may be used to notify a negative decision but the motivation given must always allow for a full justification of the grounds of which the decision was taken, and therefore indication of one or more of several options by only ticking the boxes in the standard form set out in Annex VI to the Visa Code is not sufficient in the case of refusal to issue a visa to a family member of an EU citizen.

So if she hasn't done so: appeal, complain with the embassy (and EU Home Affairs, the ministry the embassy fals under and possibly also the EU representation in the Philipines), ask the money back, the visa was refused on incorrect grounds. etc. The handbook and early provided links should give all the hints and pointers required. Too bad some embassies (Schengen but British too) are doing poor jobs when it comes to applying EU agreements, treaties, directives etc. correctly.