I'm sure the confusing/misleading marketing hurt it, but imo it was just one of the blandest and most disappointing films Pixar has ever made. And it's not like it didn't have some interesting ideas, it just didn't know what to do with them.
Also, I think animated sci-fi that tries too hard to be just like live-action sci-fi is just not clicking. It's why I think Elio might actually do well, that one seems like it can only be told in that medium.