Ok here is the logic
The manufacturer probably specified a 50 amp breaker to reduce trips during the startup inrush. You all know an a/c has a large inrush current.
Now if you are using a 50 amp breaker you MUST use #6ga or larger wire to be safe and meet code.
The breaker and wire size must match to be safe.
But it does seem the directions were confusing re the number of conductors needed.
6-2 is three total conductors, 2 that carry current and one safety ground.

Mark