Kryten says that the last time he used his auto-repair function was during the visit to the Esperanto (in "Back to Reality"). However, he actually used it more recently than that, in "Psirens" when he is forcibly trash-compacted.
Lister's head is not aligned with his new muscular body which makes it obvious that it is not his real body.
When Lister steps off the vertical medi-bed with his new musclebound body, in the shot where he stands in front of Kochanski with his back to the camera, the body double has a very square jaw that looks completely different to Craig Charles's.