It's happening for me too!

Is there another way to remove the HUD around the pokemons and or the black shadow bellow the pokémons?

A recent TTS update has caused something screwy to occur with the models if their bases are removed now. There is a workaround however! The broken texture parts are actually tintable, and are overlayed on top of the actual model's textures. If you tint the model a grey-white (the tint option is in an object's right click menu), the issue becomes practically invisible, re-revealing the correct textures underneath.

Charem thanks!, i´m here for the new issue. I use the models without bases but now are broken textures. I change with grey-white tint and now looks better

@Charem thank you!

Charem, ty. Worked nicely here. Used html color #CBCBCB

Just wanted to let you guys know, tinting the bases white-grey doesn't work for every model, you have to check every one individually, the reason I found this out was because of Kyogre, I can't recall if it's the regular form or the Primal Form, but the red lines going up Kyogre's dorsal fins gets overlapping textures with the base, for Kyogre you'd need to tint the base red for example.

That is gold information and sad news. Thank you, MrZangetsu!