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 refresh.