Why did my roasted butternut squash ferment?
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.