The courts have the final say in a judicial recount. Even if the reason the vote wasn’t counted wasn’t the voter’s mistake, unless it is part of a case, in the eyes of a court it might as well be someone waving junk mail with a sticker on it.

A separate case challenging the result due to these irregularities can be brought which could end in a different outcome, but as far as things are currently, the regular election process is complete.