Why did my roasted butternut squash ferment? I roasted some butternut squash, then stored it in the refrigerator for a few days before I had time to puree it all.  When I pureed it I discovered that it had fermented.  What caused this to happen?  It smelled and looked fine, but the bag I stored it in kept puffing up and it tastes strongly fermented like I added yeast to it.
Assuming you cooked thoroughly, your squash got innoculated after you took it out of the oven. Was your counter clean? Had you just made bread? What's the history of the storage bag? Did you recently spill yogurt in the fridge?
You've got a source of contamination, and need to think carefully about everything that came in contact with the squash after you pulled it from the oven.