I used Poke Transporter to transfer pokemon from my Pokemon Silver to Pokemon UltraMoon, but some pokemon show incorrect PP in pkhex. In the game the PP show correctly.
In my Pokemon Silver, usually using TM25 ACE to clone these Pokemon, but some show PP correctly, therefore, I don't think it's the reason from incorrect PPs in pkhex
I adjunt the .pk2, the .pk7 with incorrect PPs and a imagen from the error
In the image, all legendary and mythical from gen 1 and 2 are the transfered (first 11 slots), but only Mewtwo, Ho-Oh and Celebi have errors
pk2 and pk7.zip