Did you go straight to French Consulate when you applied? Because if that's the case, they will normally asked you for requirements and will ask you lots of question...I witnessed a situation like that when I applied for my second Schengen visa.
So I suggest to use their website first,
https://www.tlscontact.com/gb2fr/login.php fill the application form,tick the right visa (spouse of an EEA national)...then book the appointment there as well. During the day of the appointment, when they ask your wife questions like where are you going, just blog it and say France (they wouldn't know it anyway) as if you would say Spain, they will ask her to go to Spanish consulate instead but of course if you already have the visa, make sure you've been to France because if not, she will be blacklisted and will have problem with applying there again. They will grant the visa very quickly, within 5 working days. Like mine last time, I applied on a Friday, passport with the visa in it arrived on a Monday.