With United already through to the knockout stages, Mourinho opted to rest a number of players for his side’s Group H finale, with the likes of Sergio Romero, Fred and Andreas Pereira all starting for the Red Devils.
Valencia found themselves a goal up at half-time before doubling their lead when Phil Jones poked the ball into his own net in the early stages of the second half.
Marcus Rashford managed a consolation goal for United with minutes remaining, but Mourinho was said he was frustrated by his side’s performance on the night.
“My team improved when I made the changes that I didn't want to make, which is a frustration,” Mourinho told BT Sport.
“I didn't learn anything from this game. Nothing that happened surprised me at all.”
Despite not being entirely happy with his side’s performances in Europe this season, Mourinho is glad United have navigated their way through what he says was ‘a difficult group’.
“Yes, job done in a difficult group. I don’t think we were brilliant in this group phase, but it’s enough to qualify and enough points with the squad we have and problems we have,” Mourinho added.
“We manage to come here tonight and to be already qualified.”
Next up for United is a clash with Premier League leaders Liverpool at Anfield on Sunday.
When asked whether he felt he could pick his side up ahead of another important match, Mourinho said:
“This is not about Liverpool today, this is about Champions League, I don’t know why you bring Liverpool in to it.
“Manchester United supporters know we go into every match with intention to win, the intention is always the same.”
“You can’t do that, it’s a hypothetical thing, you can’t do that,” he insisted.