If you are in any Qt based paint app when using X11, you cannot hover the pen over a viewport and scroll your mouse at the same time, for example, to zoom at a point. Example Qt apps: Krita, Drawpile, etc. This even happens with GIMP, even though it's GTK, so it seems like they made the same bug. It doesn't happen with paint apps running with Wine (like SAI or CSP). It also doesn't happen with apps that make their own GUIs from scratch, like AzPainter.

I also checked with evtest and I can see mouse scroll events just fine while holding my tablet pen over my tablet, so that makes it seem like the event is being dropped by Qt's event system.

However, this does not occur with Wayland in KDE Plasma, possibly because Plasma is currently treating the pen and mouse as separate "cursor" entities.

You can use other mouse buttons, like clicking, just fine. Only mouse scroll gets dropped.