That’s what Twixtor does right now when you point to a layer that has collapse transform – Twixtor clears a red frame to tell you the two frames it’s reading are not the same size. One way around is to make another precomp (precomp the layer that needs CR/CT on, leave in the precomp CR but not in the comp where twixtor is applied – clear?)
Sorry for the inconvenience, we are looking at ways to be more elegant with such case for a next version.
Pierre