I would not call it a mistake because they did not expect a shared cinematic universe to be a thing. Marvel was just trying to survive and sold rights to characters to different studios as a means to do so. Back then comic book movies were not always great. Raimi’s Spider-Man and Singer’s X-Men took some risks. They ended up being successful which lead to other movies, like Daredevil and The Punisher, that weren’t so great. If those earlier Spider-Man and X-Men films weren’t successful, then comic book movies (especially Marvel ones) might have been shelved longer, like what happened with Batman movies following Batman and Robin’s box office performance.

I'll meant they kinda had too, if they didn't sell their rights, Marvel wouldn't even be a thing right now. It wasn't just the movie that was strugging, other then the Cartoons pretty much the entirely of Marvel was struggling. Marvel's best film prior to Blade 1 was a Old Captain America Film that barely looks like the Steve we know today.

Also as said before me, Nobody would expected a shared cinematic universe to come out of Iron Man 1 of all films. Superhero Films was mostly to their selves. It was just Batman by himself or SuperMan by himself. X-Men was the first series to even hint at a Shared universe.

I mean, it ended up being the right decision in the end, and they got the rights back anyways.

No, it wasn't a mistake, it was the end result of a lot of different mistakes. Marvel was on the verge of bankruptcy and they needed to sell the cinematic rights to those characters to keep the company afloat. If they hadn't done that, Marvel would have ceased to exist and the MCU would never have existed in the first place.

Besides, if they had had the rights to Spider-Man, the X-Men, the Fantastic Four etc., we never would have seen more obscure characters like the Guardians of the Galaxy brought to the screen.