Clef change applies to both score and parts regardless of concert/transposed mode
1) User creates a score with an associated part for a transposing instrument (e.g. Horn in F or Tenor Saxophone in Bb)
2) User changes clef for the instrument in the score
3) If the score is in Concert Pitch mode and the part is in Transposed mode, the clef change impacts both the score and the transposed part, which is wrong
To be clear: a clef change to the part is supposed to affect the score and vice versa, but only for the specific mode you make the change in. So changing the clef while in Transposed mode for part should also affect the clef that appears while in Transposed mode for the score. If the score happens to be in Concert Pitch mode, you shouldn't see the change right away, you should only see it when you change to transposed mode, but the change is made. (Copied from Marc Sabatella comments on forum post https://musescore.org/en/comment/1013289 which contains more use case details as well as an attachment.)
There are two current workarounds. One is to simply always maintain the same mode for the score and part when making clef changes. The other (once bug is encountered) is to use a separate "scratch" copy of the score file for generating parts, so any such unintended changes don't affect the "official" copy of the score.