Second-half Villa goals from Ross Barkley and Leon Bailey, either side of am equaliser from Stephy Mavididi, earned the hosts the points.
Van Nistelrooy conceded Bailey's winner was self-inflicted: “It’s clear.
“You’ve seen it, I’ve seen it and the players know. So there’s no need to emphasise it. I can’t hold anything against anyone because it was an honest mistake.
“Nobody wanted to give the ball away in such moments, but it’s something you have to learn from because it’s costing you. It would have been a hard fought point away at Villa and a positive. Every week we’re getting closer to converting good performances into results.
“It’s not about blaming and pointing, it’s about handling the situation as a team and clearing away from danger. I don’t hold anything against one of my players.
“I can only praise them for their efforts for the way they played together as a team. It’s a foundation for points. They’re vital to give yourself the rewards.”
He added: “I can repeat myself from last week. It was a good performance, a decent performance. But I think through our own mistakes we let in the two goals, especially the second one.
“I think we could have done better for the second phase of the corner (for the first). These are standard situations we can handle better. In the Premier League, these situations are punished without blinking your eyes.
“That’s the disappointing bit. Because over 95 minutes, look at the possession, we were calm, composed on the ball, had some very good spells, created a couple of good chances.
“It was a very stable performance off the ball where Jakub (Stolarczyk) hasn’t really had to make a save. In general, those are a lot of positives, that are important conclusions to get points in this league. It’s just in the final details where it’s costing us against Man City and against Villa.”