Have used just for men beard dye. Now have a couple bare spots, will it come back?

You shouldn't have bare spots (or hair loss) after coloring your beard. If you are concerned see your doctor for an exam.

It's hard to say without seeing your beard. If there was local irritation, it might come back. However, if the cause of the white or grey hairs was actually a condition called alopecia areata and application of the dye caused those hairs to fall out, then the hairs might not. There are many reasons for bare patches in the beard. Please see a dermatologist for diagnostic advice and guidance. 

That is unusual. See your primary care provider or dermatologist if the problem persists. Was there skin irritation?