The foot rest is much further left and exists in both configuration so muscle memory goes to the same place to rest your left foot when you’re not using it.
The brake pedal in a manual is narrower and in an automatic it usually is the width of the manual pedal + the space between the brake and clutch pedal from a manual. If out of habit you reach for the clutch in an automatic chances are you’ll hit the brake pedal just enough to scare you.