I only started learning Unity a few weeks ago, and I had this problem with my ragdoll character. No matter what I did, it kept falling through floor. I didn't find anything on forums about this, so I'll leave the solution myself. The thing is that Animator and Ragdoll can't work at the same time. You should read about Active Ragdoll. Basically, all you need to do is turn on the "isKinematic" for all the rigidbodies while animation is on and, when character bumps into something or dies or whatever, turn off the Animator and set IsKinematic to false.
Also, English isn't my native language, so sorry if anything.
Hope it helps :)
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