People can be canonized (declared to be saints) and these official declarations are held to be infallible. Some people might be considered saints because of popular devotion, without being actually canonized - they could be "grandfathered in," rather than going through the modern process. I am aware of instances where the Church has decided that some of these people are of dubious historicity and therefore are not actually saints.
- St Guinefort, who was not only fictional, but was also a dog. 1
- St Josaphat, whose story is a fanciful version of the life of Buddha (Josaphat = Boddhisatva). Yes, Buddha existed, but the Josaphat story is not historical. 2
Has the Church ever declared "X should no longer be considered a saint" where the reason isn't "because X never existed"?
1: It's like the end of Lady and the Tramp, but seven centuries ago.
2: Also, Wikipedia is wrong to say that he was canonized: he appeared in the Baronius Martyrologium Romanum but Benedict XVI's De servorum Dei beatificatione et beatorum canonizatione says that doesn't imply canonization.