I just finished a 'screen and recoat' on the hardwood in my apartment. I screened everything with a floor buffer and 120 grit screens, and then applied a coat of sealer and 2 coats of water-based poly. I used these products:

Sealer:
http://www.homedepot.com/p/Rust-Oleum-Parks-1-gal-Water-Base-Sanding-Sealer-258687/202521769

Poly:
http://www.homedepot.com/p/Rust-Oleum-Parks-1-gal-Crystal-Clear-Satin-Water-Based-Polyurethane-258690/202521739

Most of the floor turned out great, but there are some large areas that have severe alligatoring and there are also rough patches in some spots.

Please find the images here:
https://drive.google.com/folderview?id=0B6kF0CU2nur6SE0zak9jVy14Zjg&usp=sharing

Problem#1: Roughness
These are small areas that are rough to the touch. Can I just lightly sand these?

Problem#2: Alligatoring
Most of this occurred in the kitchen where I had removed an old linoleum floor with a tar paper underlayment. Is it possible that the residue from the tar paper caused this reaction? Or did I apply too thick? Also, how can I fix this at this point?
I just applied the poly yesterday so at this point it has been curing for less than 24 hours.

Thanks so much for your help!!

You have an adhesion problem. There is some contaminant on the floor under the seal coat. You will have to go to bare wood and start again.