The Spaniard picked up a muscle injury 17 minutes into the last-16 first-leg tie and was replaced by Paul Pogba.
Herrera had returned from injury after missing games earlier in February against Newcastle and Huddersfield.
“It didn’t look like he was fully fit,” said Mourinho.
“I think he has a bad injury. He had a small injury that stopped him for the last couple of matches, but the medical department gave him 100% ready for last Saturday [against Huddersfield in the FA Cup].”
The Portuguese manager added: “He looked fit [on Tuesday] and the way he was playing during his time on the pitch – he was pressing a lot, really high – you only do that when you feel good.
“Then it was a back-heel, and a back-heel creates a contraction in the muscular area where he had the biggest problem, and now we have proof that he was not 100% fit.”
Manchester United are already without defenders Phil Jones and Marcos Rojo, midfielder Marouane Fellaini and forward Zlatan Ibrahimovic because of injury.