Shiny Mega Gyarados is still a Water/Flying type, but it has Mewtwo’s Z-sprite. Shiny Charizard x ist still Fire/Flying. My normal Mewtwo was below Gyarados, and I exported the save file.

Its still properly shiny is tickling me more than the bug itself. I have no idea what may be causing that unless its related to a visual bug ive already squashed on my dev build. After the update (soon) lmk if it happens again.

Shit. Was coming here to say the glitch was a bug in the script that got my sprites. That IS your Mega Gyarados! There just wasn't a sprite for it at all..
But when I got here, I realized you also have a Mega Charizard X that is the wrong type, and I didn't fix that... Soon. Tired. G'night.