Like a third of all the pokemon I've caught show up as invalid encounters and whatnot. I caught all of them while playing the Switch 2 version of the game, so obviously the game is being played vanilla with no mods affecting the encounter RNG. Also, most Pokemon I caught and immediately boxed and never touched again. I was using the latest public version of PKHex, V (25.10.26)b
I can't remember the details of how/where I caught them all, but most I believe I caught outside of wild zones on roofs and such. The ones I do know the particular details for are:
My Alpha Scolipede, which I caught as an alpha Whirlpede from the static alpha spot in wild zone 5 literally as soon as I could access that wild zone. Pkhex says it should have mastered spikes, but it never knew that move. It's one of my main party Pokemon and I've changed its moves a lot.
The Alpha Riolu I caught as a random alpha on the roof above the shopping mall (I forget it's name) in Rouge Sector 4 as rank E
My Alpha Sligoo I save reset to spawn and catch it as an alpha Goomy in Bleu Sector 7 near the pokemon center at the start of the day. PKhex lists it as an alpha flag mismatch for some reason. It's one of my Party Pokemon so I have changed its moves some.
My Goomy I caught in Bleu Sector 7 from the same spot as the Sligoo quite awhile sooner. I was Rank W at the time.
My Alpha Spinarak I caught in Wild Zone 4 from the static alpha spot as soon as I unlocked alpha Pokemon.
My Alpha Houndoom I caught in Wild Zone 6 at Rank E from the static Alpha spot as a houndoom.
Both Carvana I caught in Wild zone 10 the earliest time I was able to enter that zone (So Rank G or F)
My Camerupt I caught as a Numel from Wild Zone 8 at the earliest time I could access that zone (I think Rank G). I later pumped it with EXP candies to evolve it and gave it just whatever decent moves it had access too so I could beat the side mission that required using a mega one.
My Medicham I caught as a Meditite from Wild Zone 6 at the earliest time I could access that zone (I think Rank V). I later pumped it with EXP candies to evolve it (but didn't touch its moves) so I could beat the side mission that required using a mega one.
invalid pokemon (25.10.26)b.zip