When I hover over a window the border appears as usual. However, when I click on the window or interact with it somehow, it seems that the window repaints over the border and looks smaller.
This only started happening after I upgraded from bf3a656 to new commit 3e99cee.

Add yabai -m config active_window_border_topmost on to get back the old behaviour.
Does yabai -m config active_window_border_topmost on require SIP to be off?
This setting no longer exists. It was a part of the border implementtatio back in version 2.x.x.
In the latest version (3.x.x), window borders require sip to be disabled.
Most helpful comment
Add
yabai -m config active_window_border_topmost onto get back the old behaviour.