Oxford’s new head coach Liam Manning was furious with referee Sebastian Stockbridge after his first defeat since taking over at the Kassam Stadium.
Bolton secured a 1-0 win thanks to a seventh-minute strike from Dion Charles – his 20th goal for the Trotters this season – and the three points boost their promotion prospects.
But Manning was angry that Stockbridge brandished only a yellow card and not a red to James Trafford just before the break after the Wanderers keeper took out forward Kyle Joseph outside the area.
Manning said: “The performance from the referee was atrocious.
“Even apart from what should have been a red card, he was arrogant throughout.
“But that decision was game-changing. Clubs will suffer, jobs will suffer – there’s so much on the line. And he just got too many wrong today. You can’t referee a game like that, it was terrible.
“Yet as bad as the decision was, it woke us up. That first 25 minutes – you can’t start games like that. You have to step up and be brave from minute one.
“The soft goal makes it difficult because then you’re chasing the game.
“Yes, we know we have a problem scoring goals. It’s not for a lack of effort behind the scenes – we’re working on finishing every day, and have video work to try and help them.
“But it’s up to us to take the game to the opposition, especially at home. At half-time I was angry. We need someone to step up and be a hero.
“There’s a lack of quality. We need to score a scruffy one – for it to hit a player and go in.”
Ian Evatt hailed Bolton’s win as an “unbelievable result” as they were missing so many defenders.
“With four centre-backs injured you have to find alternative ways,” boss Evatt said.
“You have to show character and grit at this stage of the season, and we did that. We got ourselves ahead and managed to ride it out.
“For the first 20 minutes we were very good. But after we got the goal we almost took a step back. And overall we know we’re better than that.
“Yet for all they had the ball, and had territory, though, they didn’t really create anything clear-cut.
“I was concerned with the collision between Trafford and Joseph. I haven’t watched it back. Seeing it live I thought the touch was going away from goal, and Michael Jordan Williams was in the vicinity – but I’ve seen them go either way.
“I wasn’t comfortable when we were under pressure in the closing minutes because that isn’t the way I want us to be and to manage games.
“But at the moment we have to find alternative ways to win football matches, and if that’s the way we have to do it, to buy some time to get the other lads fit and available again to increase the strength of the group, then that’s what we’ll do.
“We said before this game we wanted to target four points from this game and Tuesday night at Burton, we thought that would be a fair return with three home games to come.
“And we’ve got three today which is huge for us and takes a little bit of pressure off us for Tuesday.
“But we also know how difficult Burton are going to be – they had an excellent result against Sheffield Wednesday today.
“But we’ll give that a real go. It’s doubtful if we’ll have others back for then so these boys are what we’ve got and they’re giving everything to try to get us over the line.”