What sort of markers are you using? Stretch markers only work for audio.
It depends on which track you are using as a time reference, midi or audio.
If you are using the audio as a timing reference, just edit the midi directly.
Hint: Select the midi track and press E to open the midi for editing in the project view, so you can see both midi and audio at once.
If you are using the midi as the timing reference, use stretch markers (or the old item split & slide method, if that suits you better) to fix the audio timing while observing its relationship to the midi track.
(and stop calling me Shirley!
)