Apologies for not seeing your question before.

It's normal to have a few holes in your emulsion; you can repair them with a special pin, use masking tape (if they're in large negative areas) or you can dabble emulsion and re-expose. If you're getting alot, then your screen may be dirty or clogged.

I'm no pro, but just keep squeegeeing on the fron then back then front, and it just kinda smoothes itself out.

Cheers.