Screws packing out on roof deck, under the rubber roof

If it's a Phillips (or Robertson) head screw, cut or file a groove across the head. After driving the screw in fully, put a staple across the groove to lock it in position. If for some odd reason you have flathead screws, you already have the groove.

Disclaimer: I haven't actually tried this myself, but have read about it. It and a few very close variations are very old tricks.