Crewe Alexandra boss David Artell felt his side shot themselves in the foot against Bolton and that Wanderers' winning goal was offside.
Wanderers travelled to Cheshire aiming to narrow the gap to the top six and keep their faint play-off hopes alive.
In a first half which was scrappy in windy conditions at Gresty Road, Wanderers improved after the break and Dapo Afolayan struck the post as the visitors looked more likely to score.
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And that late goal came when Kieran Sadlier's free-kick came off the post and George Johnston crossed back into the box for Bakayoko to net his 11th goal of the season and reduce the deficit to the play-offs to nine points with seven games of their season left.
Artell's side meanwhile remain bottom of League One and he felt his side shot themselves in the foot with the late defeat.
He believes that Ian Evatt's men never looked like scoring at Gresty Road and that Wanderers' winning goal was offside.
He said: “We shot ourselves in the foot. The best chance of the whole game after Trig (Dave Richards) has made a save from a header that he probably should make and you’ve got a one on one at the other end and not scored and then we shot ourselves in the foot.
“Any defeat should be hard to take and when it’s in the last minute it’s doubly hard. It is difficult, we all know it’s difficult. We tried playing the right way today and we’ve got a lot more to go on that front but we’ll keep plugging away with them and they’ve got to keep plugging away.
“Today was a massive missed opportunity. It was certainly a lower quality game, mainly due to the pitch which is horrific for both teams, and people say that’s an excuse but it’s a fact, it’s not an opinion.
"We’re asking them to play in a way that doesn't help but we lose the game because we shoot ourselves in the foot, I have to say.
“Don’t get me wrong, the lad’s offside from the free kick but we won’t mention that.
“There wasn’t enough quality in the final third. The pitch doesn't help but we’ve got to do more. We have got to do more. The best players were the back players, the man of the match was one of the back players without a shadow of a doubt.
"I’m not taking anything away from Tom (Lowery) but he didn’t create or score a goal so he shouldn’t be man of the match. He’s fine but with the back players, Bolton never looked like they were going to score a goal.
"They’ve had one chance in 90 minutes and you’d take that in every game, wouldn’t you, but you want players to create and score goals and we didn't have enough of that on the pitch.”
“It was a free kick but it should never have been a free kick because their lad shouldn’t have been allowed to get there.
“You’re obviously fearful when there’s a free kick on the edge of your own box but I never felt that Bolton were really going to score a goal today."
