if you're checking on PKHeX, and it flags a mon illegal, and it's a mon you're able to legally catch in those games, then it almost certainly happened.
To use RNGreporter to compare spreads wouldn't exactly work: you'll need to knowledge of whether the game skipped frames to begin with,
and you normally wouldn't be able to know if the frame skipping is natural consequence or the emulator mucking up.
To provide context, this works when a mon's encounter is only allowed to be Method 1 (for example), and it instead got Method 4.
If a mon is allowed to have Method 1, 2 or 4, then it would show up as legal either way.
I'm sorry, but if I'm not mistaken, system date doesn't matter, since we're talking about GBA games. GBA doesn't contain system dates?
In any event, you're not using distribution carts, so no need to dig into this.