Look at screenshot:
You will see a note, displayed in midi editor window, but not displayed in arrange.
This note is not played - this is how I found this issue.
The reason is shown on second image:
I moved a start of mentioned note to show underlying "garbage" note.
This additional "garbage" note ends quickly, that's why in overall it sounds like missing note.
Nothing special here so far.
But the issue here is that both views are inconsistent in what they are presenting.
Question remains: which view is most proper: this which shows note being muted, or this which doesn't show one even if it does exist
BTW is there any way to avoid such overlapping notes? It's not the first time I noticed such situation.