What's wrong with the polyurethane on this hardwood floor refinishing job?
There is something...in those pieces of wood.  (Detailed enough for you?)  

Ok, so I would have initially said temperature until you mentioned it was only specific pieces, which leads me to think moisture, but even that would cross pieces...

My best suggestion is sand those spots down, clean them with a solvent dampened rag, lacquer thinner maybe (don't pour it on) and then apply a wood treatment to the spots.  Then re-coat.

Edit:  To answer your question in the comments

Yes, should have mentioned that, you will need to sand before completing the steps I outlined.  If it isn't real wide spread I would just use scraper to get the big chunks off and then a fairly fine grit sandpaper and do it by hand.  If there is a lot I would go with a palm sander or belt sander.  You don't want anything that spins it will leave marks that will be visible in the final finish.