Does anyone else play a character that this affects on a regular basis? Let me give an example if you are confused.
Go pick Cody, then pick Akuma or Dudley or any number of characters in training mode. Have Akuma crouch while do you perform far standing heavy punch over his head. The move will whiff around 70% of the time and hit around 30% of the time even if you stand in the exact same spot. The reason being that the hitbox for the character sometimes moves slightly up during the idle animation since the characters are animated to look like they are breathing or something.
The fact one of your tools might not work for a reason that isn’t related at all to game balancing is really annoying. If it didn’t work AT ALL it would be less annoying, but for both the player using the move, and the player on the recieving end of the move, having the random chance it might work or might not is even worse.
Cody has a number of these types of things (he also has a number of normals that just flat out whiff on certain crouching characters but not others, his far s.HP far s.LP close s.LP close s.HK and close s.MK will all whiff on a crouching Honda (sometimes the close MK hits but sometimes not) but all of them hit a crouching Seth.