I trained and evolved my Caterpie with the Hidden Ability(Run Away) into Metapod, Metapod only has the Ability Shed Skin, after I evolved the Metapod into Butterfree it lost his Hidden Ability(Tinted Lens) and got Compound Eyes instead. I tried the same with Wurmple into Dustox and Beautifly the Hidden Ability was lost aswell so I tried more with Weedle into Beedril, the Hidden Ability was lost again. I tried it a couple times all of them lost their Hidden Ability.

Hi there, apologies on the late response here,

I've confirmed the same thing is happening on version 9.1.3 - it seems any time a middle stage pokemon has no hidden ability but the first and third forms do, the HA "status" from the first form is lost. This impacts at least Metapod, Kakuna, Pupitar, Silcoon and Cascoon.

Moving this issue to internal now so it can be resolved, thanks!