Wootton says United were unlucky to lose and could have perhaps won the game by a margin.
"It felt great, it's another first team start and I'm delighted about that," Wootton told MUTV. "But obviously the main thing is the team and we are all disappointed that we lost the game, even though we'd already qualified.
"We created loads of chances and on another night, with a bit more luck, we could have been three up by half time and the game could have been out of sight. Thankfully, we were already through and there was no pressure.
"There is nothing you can do about goals like that. Fair play, it was a great strike from their player. It was probably the biggest game in their history so to come to Old Trafford and get a win in front of a near full house was massive for them, fair play to them, but we're very disappointed.
"Our players are very professional and we want to win every game we go in to. I don't think it was anything to do with a lack of effort or anything like that. Like I said, with a little bit of luck and if we were a bit more clinical in front of goal, we might have won by three goals."