Problem Invalid: Encounter Type PID mismtach (3gen)

Hi, I have a question, I have reviewed my 3 gen pokemon with pkhex, and mentions that : Invalid: Encounter Type PID mismtach , in all those that I show in the images. I play in emulator, but all of them have been captured legally (also with the whole game), I have not used any hack or code, it is a bug of pkhex ?, can be solved ?. This being honest to say that all those brilliant ones I got them without using rng reporter or creating them through pokegen or pkhex. I just feel that

Because some are legal, and some are not. Certain encounters have certain PID restrictions (ie a Starter / Stationary encounter must be Method 1) while wild encounters can be Method 1/2/4. The method-1 only encounters are generated fast enough on actual hardware, but the emulator does not generate the pkm fast enough and gets interrupted, resulting in method 2 & 4. Wild encounters need to wait for a valid PID (nature/gender) which can also be interrupted by the screen needing to re