Holloway felt his side should have been awarded a penalty following a clumsy challenge by Rafael on Luke Varney shortly after half-time.
Holloway told his post-match press conference: “How disappointed am I that my lads have given that effort, absolutely flat out, pedal to the metal? How can he not see that’s a penalty?
“You have got to give them (United) credit. Substitutions on the night, they have got such a great squad, their attitude, everything about them is fantastic.
“And the tempo that they close you down at, my team wasn’t used to it. The last time we faced that was Chelsea and they whooped us, and Arsenal and they absolutely murdered us.
“We have just done that to them (United) and it’s 3-2. We could have gone 3-0 up and, do you know what, it wouldn’t have been undeserved.
“So, I think we have come a long, long way. I’m sorry that I feel a bit down. Sometimes you need that (the penalty decision) to go for you to convince the lads.
“But I’m sure they know how well they’ve done and how proud I am of them. I’m sure the more I keep talking about them people will see what I see and they will actually get some credit.”