GarageBand has this quirky thing... if you select a note and copy it, but forget to move your red marker to the place you want the new note before you habitually press the apple-V shortcut to copy it, GB pastes the new note right on top of the old note. So there's a possibility that you have a hidden note behind the MIDI note you see. I call this a "ghost" note. No idea what the proper word is, but hey, this describes it well.
To check to see if this is the problem, in your MIDI track's Piano Roll (shown after hitting the "snowflake" in the bottom left corner):
1. Select the problem note and drag it upward or downward.
If there's a "ghost" note, you'll see that copy still in the place from which you just moved your note.
2. If yes, there's a "ghost" -- just delete the note you just moved.
3. If no, there's no "ghost" and you need to keep investigating, just do an
Edit > Undo change position of note (or the more common apple-Z shortcut).
Then you're back where you started from but have ruled out a common-enough cause of muddy notes.