it looks like ballots can only be challenged before they’re counted, which matches with what you just said.

I mean, in the US specifically, and everywhere else, they can be disregarded for not being valid during the counting process, see :

https://en.wikipedia.org/wiki/Chad_(paper)#2000_United_States_presidential_election_controversy

or, if you're more degenerate:

https://balatrogame.fandom.com/wiki/Hanging_Chad_(Joker)

EDIT : thank you for being polite, you're welcome for my explaination.