According to this article on cmuse.org,
Even though Mozart is the only Western musician and composer who was explicitly acknowledged as having perfect pitch, Bach, Händel, Chopin and Beethoven are generally known to be endowed with that ability as well.
So, it is never explicitly said that Beethoven had perfect pitch. Though it is suggested, it’s not confirmed – meaning that it’s possible that Beethoven didn’t have perfect pitch, but perhaps very good relative pitch.
Therefore, is it possible that Beethoven “heard” with his inner ear the pieces he was writing wrong? For example, his 9th symphony in D minor – could he have “heard” it completely different to how we hear it?