Did you explain in the cover letter the reason for her to return back to the phils on or before her visa expires? They are very hot on this topic ang like what other said visit visa can be very unpredictable.

If you going to re-apply for visit visa, i suggest that you point out in the covering letter the reason why she needs to return back to the phils, i.e school, work and provide documents to support them.

Also, she dont need to book any hotel if she goes manila/cebu to apply, Ive done many roundtrips before from Dvo to Mnl in a day just to lodge me app and it all worked, she just have to manage her time wisely.

Dont lose hope yet, Im sure there will be ways to let her see your hometown. Best wishes. Xxx