Derek McInnes felt Motherwell stopper Shaun Hutchinson should have been sent off in at Fir Park.
Russell Anderson's late leveller and a debut goal from Adam Rooney cancelled out efforts from Stephen McManus and Zaine Francis-Angol.
However, the Dons boss was upset after Ryan Jack was taken to hospital for x-rays due to Hutchinson's challenge.
He said: "I'm really disappointed with the challenge, I thought it was an awful challenge."
It leaves the young midfielder a doubt for next week's Scottish League Cup semi-final with St Johnstone at Tynecastle, a game of huge importance to the Dons as they bid to end their 19-year wait for a major trophy.
"He's been to hospital, he's had an x-ray, so we'll see how he is," McInnes told BBC Radio Scotland.
"I think there has been a touch involved from the defender but it's only a challenge that's going to hurt somebody, and it was a terrible decision to not give him a red card, and I'm disappointed in it."
The Dons recovered from the early loss of Jack to dominate the clash between the two sides vying for second in the Premiership.
Aberdeen twice found themselves behind and captain Anderson had to bail them out when he bundled Niall McGinn's stoppage-time corner over the line.
"The two goals we lose put a black mark on the actual performance because obviously we're disappointed with them, but I thought it was a decent performance from us," said McInnes.
"It had to be to get something from the game. When the clock goes up for injury time and you're behind, to get a point you're always pleased.
"I always feel there's a goal in us, and the players deserve huge credit for that. They keep going, there's good perseverance and good determination, and they never accept it.
"I thought it was some good play from us as well to get into good goal-scoring positions.
"It wasn't frantic, it wasn't just lumping it, there was a measure to our play in the last 15-20 minutes after going 2-1 down."
New signing Rooney was pitched in from the start, and took just over an hour to break his Dons duck, heading into the net after goalkeeper Gunnar Neilson had parried McGinn's effort.
"I thought he was excellent," said McInnes of his new striker.
"He led the line well, was on the move and was lively. He was giving the centre-halves a tough time, he was moving them about and not standing still, and I always thought he looked likely when the ball came into the box.
"It was a great reaction for his goal."