Pretty sure they mean that 2 objected/rejected the letters because this happened to me for a very small subset of schools as well. Einstein was definitely one of them, and they were not super accommodating when I wasn't able to reach one of my letter writers--I basically had to use another letter writer to satisfy their requirements of who you submit letters from, and it was only by luck that I was able to--and then I didn't get an interview anyway. Otherwise, I think it's likely that in practice, at most schools, if one letter is on the wrong letterhead it's not a huge deal. That said, I wouldn't be surprised if it causes it to just be ignored at certain schools and they don't even bother to tell you or contact the writer and just move on evaluating the app without it.
It also certainly can't help your application in any way, so I would suggest you try to have your writer re-upload on correct letterhead.