I've noticed the L-menu toggle for Non-Vanilla types isn't affecting Vibrava and Flygon. Trapinch gains/loses it's Bug typing depending on the setting, but both Vibrava and Flygon are always Bug/Dragon. I haven't noticed this happening to any of the other pokemon with changed types so far.
If it helps for troubleshooting, I'm using MelonDS on Windows and my EoS rom is patched with the latest Alpha 3.0.3 patch. My save was originally started on the first 3.0 release, though I've been keeping up with new versions of the patch as they've been released.