Remember that the puppet tool initial mesh is generated from the alpha of the layer that is active when you apply the first puppet pin, so it could be problematic to have layers that have very different outlines in the timeremapped comp. The best solution i know for this is to make a fully solid layer when applying the first pin to force the genearation of a puppet mesh that fills the whole layer, this ofcource also looses some of the deformation beauty of the puppet tool, but you will never get cutoff layers either.
Maybe other have another better solution?