I don't think this is a bug; as far as I know, subbing out a player at around 60' is only going to save you 1% or maybe 2% condition loss compared with playing the whole game. So if this player was the lowest at the start of the match (by 2% or more) then he'll probably still be the lowest at the end, even if you subbed him out. You do know that you can increase the condition of a player by 2% for 80 energy, using the activity tab on the player page, right?
