Wanderers defender Eoin Toal is likely to miss the remainder of the campaign due to an ankle injury.
The defender was forced off during the second half of the 4-0 win against Plymouth in the Papa Johns Trophy final at Wembley after a reckless challenge by Sam Cosgrove.
Toal had become an important member of Ian Evatt’s side since breaking into the first-team picture back in December.
The 24-year-old will now miss some important fixtures as the Whites aim to maintain their place in the top six and push for promotion to the Championship.
Cosgrove was shown a yellow card by referee Ben Toner, and current rules mean the FA are unable to look at the incident and issue a retrospective punishment.
The Bolton boss said: “I just think the tackle was an absolute disgrace. The fact that he wasn’t sent off – and because of the rules the FA can’t look at it – is just completely wrong on every level and we have to look at it.
“In my opinion, he has gone to hurt an opponent. My player, who was outstanding in the final and has been outstanding this season, is now going to miss real key games from someone else’s stupidity.
“I don’t think the official got it right on the day and I don’t think the rules are right that if an official sees it and brandishes a yellow card, they can’t retrospectively look into it.
“(Eoin) is really sad, disappointed, upset and angry. He has every right to be. Everyone has seen the tackle, there is no excuse.
“It also means we are very light in that area with key games to come. If we get any more then we are going to be struggling. As I said, it is a massive frustration of mine and the only real negative from the day.”
One silver lining for Wanderers is the return of George Johnston, who came off the bench against the Pilgrims.
The defender had spent several months on the sidelines with an ankle problem suffered during the 2-1 win at Charlton. Prior to the injury, Johnston had been one of the Whites’ most consistent performers in League One.
“I am all for full-blooded tackles, I was one of those players,” Evatt added. “I am all for the spirit of the competition, but it was clear what that (tackle) was to everybody.
“The fact there is going to be no punishment moving forward doesn’t sit right with me.”
Luke Mbete is another option at centre-back, having made seven appearances for the Whites since joining on loan from Manchester City during the January window.
The youngster was left out of the squad against Plymouth at the weekend, and the boss admitted it was a difficult choice.
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