Skipped steps while ramming, with wipe tower no sparse layers
I was lucky enough to notice the layer shift while its origin was still on top.
I had turned the wipe tower to be along Y and shortened it. "No sparse layers" was on (experimental in PrusaSlicer 2.9.5), so there was time for the nozzle to ooze during descent. The shift happened during the first color change, on top of a solid first layer. 0.2mm SPEED PLA @ MK4S, 250% extra flow for purging, 150% wipe tower purge lines spacing.
The extruder started its ramming moves in the lower right corner of the photo. The Y motor appears to have skipped near the end of the second pass, nozzle moving "downward" in this photo. The ramming passes to the left of this were after the shift and extend off the end of the tower. The only other filament laid on top of the "scene" is the brown wipe tower shell.
I can't explain why that second pass extends so far beyond the later, shifted passes. I would have guessed the motor was finished skipping by the end of that pass and so the nozzle wouldn't have gotten that far. If it was there to begin with, that might explain the skipping.
As yet I haven't tried to reproduce the issue.