Before you slip-edit the edges of the residual clips, what are their start and end times relative to the loop/punch end point, and how long are they in samples?
I just did over a hundred takes of a one-bar auto-punch with Overwrite and On Stop Rewind to Now enabled, recording to take lane two of three created in advance. I randomly stopped and restarted takes everywhere from during count-in to after the punch range and did not generate any residual clips. I did another 50+ using a fractional tempo with an un-snapped Auto-punch range that was a few ticks longer than a measure, and still haven't seen any weirdness.
Assuming it's not totally random, what I'm wondering what you might have been done differently to stop recording the takes that left residual clips or to start the next take that should have overwritten them.
The only scenario I can think of is that if you shortened the Auto-punch range somehow between takes, the next recording would not overwrite the end of the previous one. But even when I do that deliberately, shortening the punch range by one tick, the residual clip from the previous take doesn't look like what your screen shots show; mine has smooth edges at all zoom levels at which it's visible.