Refinishing floors - wood has blotches where filler was used - need advice on how to fix
You'll need to start over, sanding out the splotches of glue.  To deal with the divots of glue, they can be 'set' using a nail-set in the same manner that you'd set a nail ... or the divots of glue can be dug/scraped out ... or simply left as-is. 

You'll likely have similar splotches with store bought wood filler, and blotches can arise from other contaminants as well.  One option is to re-sand, removing the existing splotches of glue, then apply a coat or two of the poly.  This will seal the wood, then set/refill the divots if/as desired. As an alternative treatment, the divots can be blended in with a faux-finish by using a small artist's brush and a few tubes of artist's paints.  Then apply your final coat(s). 

Sorry for the bad news.  Glues and fillers are a bane to fine woodworking.  Take a week or two for a breather and regain your motivation to do a good job.