Stems point in the wrong direction after transposing

Perhaps the stem directions were set to up or down rather than auto before transposition, in which case, the setting is preserved.

You can select all the notes. Right click on one note and in the pop up menu use Select Similar. You can restrict it to just one stave with Select Similar on this stave, or more clever things like all notes with this pitch using the other options under "more". If you select a range first by clicking on the first note and then shift clicking on the last note in the range you can further restrict your selection. See https://musescore.org/en/handbook/4/selecting-elements for more detailed information about how to select things.

I think Control/Command+r reverts stem direction to an ideal/default position. If this works you can select a wide range of notes, an entire staff, or the whole document and apply Control/Command+r

Note that this will remove any hand edited stem flips.

... and Ctrl+A is the shortcut to Select All. (As it is in many programs)