Some skull fragments in the Russian Archives, previously thought to be Hitler's, were later found to be a woman's. There are also fragments of jaw, which Hitler's dentist certified in 1945 were indeed Hitler's.

The remains aren't really that important, though. We have several accounts from witness who personally saw his dead body and cremation. OK, in theory they could have been lying to enable an escape, but several factors render this realistically impossible:

• None of the eyewitnesses have ever recanted, even after it would have long ceased to benefit them to maintain the lie. Otto Günsche, for instance, who claims to have personally discovered and carried to the surface Hitler's body, lived until 2003, long after Hitler would have likely died of natural causes anyway.
• It assumes Hitler could have got out of Soviet-encircled Berlin with no-one noticing, which is unlikely.
• No-one ever found any evidence that he was in say, Argentina. This is in stark contrast to the considerable evidence and knowledge that Mossad collected on the whereabouts of Mengele, Eichmann and several other minor Nazis who managed to escape.
• Several Soviet agents are reported and testified to having exhumed and reburied Hitler's body.

Most of the conspiracy theories about Hitler not really dying comes from the Soviets initially being very secretive about it in order to play mind games with the Western allies and cast doubt on it. But they knew for certain he was dead within a fortnight or so of it actually happening, they just didn't let on for a while.