I am having the same issue. Source footage is Canon 5D h.264.
I am also conforming the 29.97 clips to 23.98. (Both by just dropping the 29.97 into a 29.98 comp, and also using the interpret ftg dialog)
Files appear correct upon re-import into after effects, but QT and FCP and Resolve show the wrong TC.
Strangely, both QT and FCP playback at the correct 23.98 fps, but the frame count goes through 29 frames.