Update: nope, it looks like it's still occurring, and it's specifically a problem with Verbatim mode.
I had tested the bug both with and without Verbatim mode — I thought — and it was present in both, and this afternoon it was not present in either. However, it turns out that when I changed between modes, Kagi didn't actually apply the setting, despite appearing to.
To sum up: This is a Verbatim Mode bug, and it is still present.