For some reason PKHeX shows some of my (mostly) static Pokemon as illegal with the error shown below:
All those shiny Pokemon are caught 100% legit via RNG manipulation. No hacks involved, etc.
PKHeX decided to mark some of them as illegal for some reason like my Kyogre and Rayquaza, while Groudon for example has no problems. Makes no sense, all of them share the exact same shiny frame.
Another example is the Swampert line (also shown in the pic) which was my starter and also got RNG'd legally to be shiny which appears as illegal again in PKHeX, while later I got shiny Torchic line of the same frame which appears as legal.
[for anyone wondering: 1) I got the whole line through the cloning glitch (yes I kept the Starter first form up until Battle Tower). 2) I got Torchic by using Gen3 ACE to re-enable the Birch-Bag event to get another Starter. Again, 100% legit Pokemon, NO reason to be flagged as illegal (Actually the original Starter Mudkip flagged as illegal while Torchic is not go figure..)