Let the floor dry between coats at least 24 hours? Lightly sand between coats? Clean the floor after sanding? Let the floor dry after cleaning? Mix water-based poly with oil-based poly? Stir (not shake) the can of poly?
If you answered Yes, Yes, Yes, Yes, No, and Yes to these questions, then I can't figure what happened. If you answered the respective questions DIFFERENTLy with their respective answers, 'that' could be the cause of your woes.
There are plenty of sources for how to 'properly' stain and finish a floor. (It's Aaaaaaall over the WEB.) If you need any refences, let me know. You might want to re-read the can to see if you missed anything the mfgr. of the finish had suggested/recommended.