Javier Hernandez and Robin van Persie were guilty of missing the best opportunities for the visitors in the UEFA Champions League clash, with the Dutchman also seeing a second-half penalty hit the post.
United's disappointment was compounded in the closing minutes of the match when Marouane Fellaini was sent off for the first time in his Old Trafford career.
Moyes felt that his side had wasted the opportunity to move clear at the top of Group A, although he remains confident that they will still be able to secure qualification for the knockout stages.
"It was a game we should have won, it was there for us to take the points and get ourselves in a really strong position and get clear," he told ITV Sport.
"We've not done that but we're capable of doing it in the other games as well.
"We're still top of the group and we're in a good position, (but) we should have taken three points."
The Scot also leapt to the defence of Fellaini, insisting that the Belgium international was unlucky to be shown a second yellow card for a late challenge.
"I think there were some strange decisions, and that was one of them," the United boss added.
"I think it was just a case of totting up (the challenges) at the end of the day that got him the sending off.
"It was harsh, as he played well."
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