I managed to track it down further. The issue is that some icons (Discover, Gajim, Steam) pull their light/dark info from the “Colours” instead of the “Plasma Style”. So If you mix and match like I did (Breeze Twilight, i.e. Breeze Dark Plasma Style with Light Colours), then most icons will appear light due to the Dark Plasma Style, but some will be dark because they get their Light/Dark info from the Light Colours.
That information seems to be cached in ~/.cache/plasmashell/qmlcache/. When I delete that folder I get the broken icons. I f I use the cached folder from my desktop it’s fixed. I’m guessing some apps just are broken currently in that regard and I’m just “lucky”, that my desktop didn’t correctly flush the plasmashell cache