Hi,
this weird sounding problem is related to an incorrect move notation imported from some PGN files.
Some PGN files out there on the web do not have correct move notations for ambigous moves under certain circumstances. The long notation (Nd4-es) is only correct, if really two pieces of the same kind can move to the same square. However, if one of the two is pinned and thus can't move it is not correct to use the long notation. CPT expects always 100% correct PGN notation.
In case this is the problem you happen to experience then you have to get rid-off of this incorrect move notation. I can't test it myself right now, but there might be two solutions to this problem.
Easiest solution: Delete the move in question and re-enter all moves which depended on the move as well as the move itself.
There might be a better approach, but I can't test it right now. Go to the position where the move with the incorrect notation is played. Drag & Drop the move yourself during edit-mode. Go back to the position. Now, if you are lucky (can't test it right now) CPT added the move with the correct notation beside the incorrect one. If this is the case you can just delete the incorrect one and you are done. Thanks to transpositions the other moves which depended on the incorrect move should remain as the newly added one leads to them.
Please let me know if any of the two works for you.
You might want to make a back-up of the repertoire before you start with the experiment. CPT has a build-in ZIP functionality which you can find under "File".
Regards,
Stefan