Not able to replicate the issue... but noticed that you've got 4 channels (that;'s tracks 6, 7, 8 and 9) muted in the Mixer.
So, as you may be aware it's possible to have different Mute levels (sorry - really don't want to add to the confusion... but it's true!)
Basically, it's possible in Logic to mute the channels strips independently to the tracks in the Arrange area...
Also, it's worth bearing mind that if you for example copy an audio region and the playhead moves over the copy immediately after it's been copied... you probably won't hear it being played back immediately. Logic's audio engine has a slight lag. So, yes, hitting stop and play again will resolve that issue.
Hope this helps