sometimes Sage adds good comments to their programs other times they do not. This is a case of not so much here at all.
From walking backwards through the code (version 2016) the count (4158 in your the screenshot) is how many records are found in IM_DataEntryCostCalCommit table that match the tiers you are updating during physical count entry. I've read the code in the subroutine over and over and I'm pretty certain that the number reported is just how many records match and not how many were ""cleared"" I can't read the programmers mind but the counter is incremented as soon as a match is found not when the commit is actually cleared farther down in the code. So it looks to me like the message is supposed to tell you us how many records were cleared which would be ""unexpected"" when updating physical count entry. most likely that counter was moved and used for some other purpose but the message in the code for Physical count update is still reporting these as unexpected.
I'm doing quite a bit of speculating but that is what it looks like without actually breaking into the code while it's executing.