I know what you mean, it's ridiculous. I'm playing as Atletico Madrid and at least 6 players per game have no stamina after about 70 minutes, even if i try and conserve energy.
It does effect the AI players as well, just played Barca and Messi and Neymar were knackered. It's so unrealistic as well, professional players don't run to a stand still with 20-30 minutes to go, yes they may be a bit tired but not to the extent that is represented in the game.