I posted a reproduction of his first translation, which the Catholic Church tried to stop & burn. His revised edition, a few years later, DID have notes...and the Catholic Church ALSO tried to suppress it.
However, since they tried with equal vigor to suppress his translation, both with and WITHOUT notes, it seems pretty obvious it was the TRANSLATION they objected to, not the notes!
If by "they" you mean the English church, they objected to both. But merely translating the Bible didn't make one a heretic. If done without approval, it made one an unauthorized translator.
If by "they" you mean the people in Belgium who put him on trial, they didn't care about his translation into a language they didn't speak one way or the other ... and that was reflected in his indictment.