Slot’s side returned to winning ways having lost their previous four games across all competitions with a relatively comfortable 5-1 win over Eintracht Frankfurt.
British record signing Isak, 26, started the game alongside Hugo Ekitike up top but was brought off at half time.
Speaking to TNT Sports after the game, Slot confirmed that the Swedish striker had to be taken off with a groin injury.
"Hugo got a big chance and he scored it," he said.
"Alex got a few. Unfortunately he didn’t score yet, but he had to go off at half-time because he felt his groin a little bit. That’s a pity.
"I’ve said it many times, it’s such a difficult balance to find with a player that missed out three months. You bring him slow, you bring him slowly.
"People also maybe sometimes argue with me if you cannot play him more or more often, no longer.
"Now we've played him for the second time in three days and unfortunately he had to go off, so let's hope for the best.
"But it's it's not an easy balance to find if a player has been out for so long."