Why Does Stroke Do This?

R,

In addition to what Monica said, there are (also) unneede/unwanted Anchor Points on what ought to be straight segments, 5 of them being directly visible in the screenshot.

That white path ought to have only 9 Anchor Points at the corners, and any number beyond that makes it less clean.

You can remove the visible ones, and then look for the remaining one(s) at the corners. One way is to deselect, then Click each (top) Anchor Point with the Direct Selection Tool and press one of the Arrows on the keyboard for an incremental move to reveal whether there are two, then remove the unwanted one if any; you can reverse the incremental move; and Ctrl+Z for Undoing is your friend.

Stroke only does what you ask it to, and sometimes it can help discovering discrepancies that can otherwise cause trouble.

There could be duplicate anchor points in that corner.