Ok, I was doing Belsavis Dailies on Republic side and in one of them you need to destroy that rakata in the mind trap but before that you need to fight bunch of Flesh eaters. Is it answered anywhere why and how they are there? Weren't they supposed to be only living in Tython?

In a JC story scene on Tython, it is implied that the flesheaters were the servants of a group that had allied with the "dark side" faction during the war at the beginning of the Jedi Order. However the masters of the Flesheaters vanished before the battle actually began. Putting that together with the presence of flesheaters on Belsavis, I think it is safe to assume that the flesheaters were servants of the Rakata, so their presence is possible in any location where Rakata were present.