My wheels are picking up little sticks and twigs on the train and tossing them at my son's bike following behind. It's not unreasonable at all that something got caught you didn't see and then it was gone.
I've pulled a presta valve out of the tube before with an air chuck that didn't release.
I use the nut. It keeps me from shoving the stem into the other side of the tube when putting the air chuck on them. But if you don't like them, you don't have to use them. Many don't. Matters not to me what you do for you.