Bury scored a contentious late winner, as Rovers slipped to a 1-0 defeat in their second Checkatrade Trophy group game.
After a goalless first half, in which Danny Graham had a couple of decent opportunities to open the scoring, Bury grabbed the only goal of the game 12 minutes from time.
Harry Bunn saw his initial header saved, but he bundled the rebound over the line, despite Andy Fisher appearing to have two hands on the ball.
Rovers pushed for an equaliser in the closing stages, but the Shakers saw the game out to secure the points.
Ahead of the game, manager Tony Mowbray named a much-changed starting line-up, with 10 changes to the side that defeated Gillingham 1-0 at the weekend.
Peter Whittingham was the only player to keep his place from Saturday's game, whilst Danny Graham, Ben Gladwin and Craig Conway, who captained the team, were the only other senior players on show.
The rest of the side was made up of youngsters, with defenders Sam Hart and birthday boy Matthew Platt making their first starts for the club.
Every outfield player on the bench were members of Rovers' Under-23s, including five players - Connor Thomson, Lewis Mansell, Joe Rankin-Costello, Stefan Mols and Lewis Hardcastle - who were named in the senior squad for the first time.
Charlie Mulgrew, Corry Evans and Jayson Leutwiler were away on international duty, Paul Downing was ineligible, whilst the likes of ex-Bury men Paul Caddis and Elliott Bennett, as well as Derrick Williams, Richie Smallwood, Bradley Dack, Dominic Samuel, Marcus Antonsson and Elliott Ward were all given the night off.
There was little to choose between the two teams in the early exchanges, with Hart seeing a shot blocked on 10 minutes and Greg Leigh heading a Chris Maguire cross wide of the target 10 minutes later.
On 24 minutes, Whittingham played a superb through ball to Graham, who looked to be clean through, but Eoghan O'Connell just got back to make a goal-saving challenge.
The best chance of the half arrived just a couple of minutes before the break, courtesy of a Rovers counter-attack. Conway slipped in Graham, who forced a fine fingertip save from Leonardo Fasan with a crisp left-foot strike across the keeper.
Straight up the other end, Jordan Williams crossed from the right and Michael Smith's near-post flick was saved by Andy Fisher at the second attempt.
Rovers registered the first attempt of the second half, but Conway's curling free-kick went just wide of the right-hand post.
Mowbray made a double change on 57 minutes, as he looked to spark the game into life, with Rankin-Costello coming on for his debut in place of Harry Chapman and Joe Nuttall replacing Graham.
A minute later, Rovers came close to breaking the deadlock in fortuitous circumstances, as Conway's mishit cross almost sailed into the top corner, but Fasan showed good agility to tip the ball over the bar.
On 64 minutes, Mols came on for his debut in place of Conway.
As the game started to open up, Ben Gladwin's shot on the run from 25 yards out forced a smart diving save from Fasan, whilst Maguire and Harry Bunn both fired efforts straight at Fisher at the other end.
The visitors were gifted a great chance to open the scoring on 70 minutes, but Maguire's attempted lob over Fisher landed on the roof of the net.
The breakthrough did arrive 12 minutes from time and in controversial circumstances. Smith sent over a cross from the right, Bunn's downward header was saved by Fisher, but the Bury player slid in and forced the ball over the line.
The Rovers players appealed for an infringement, as Fisher looked to have two hands on the ball, but referee Scott Oldham awarded the goal.
The hosts pressed for an equaliser in the closing stages, with Mols firing a shot just wide from the edge of the area and Nuttall heading wide, whilst Fisher made a superb point-blank save to deny Leigh at the other end.
ROVERS: Fisher, Travis, Nyambe, Platt, Hart, Chapman (Rankin-Costello 57), Harper, Whittingham, Conway (Mols 64), Gladwin, Graham (Nuttall 57).
Subs not used: Raya, Thomson, Hardcastle, Mansell.
Booked: Platt, Hart.
BURY: Fasan, Leigh, O'Connell (Shotton 69), Maguire, Williams (Humphrey 79), Reilly (Tutte 82), Edwards, Skarz, Smith, Ince, Bunn.
Subs not used: Maloney, Beckford, Ajose, Dai.
Booked: Skarz, Williams.
Goal: Bunn (78)
Attendance: 2,025 (230 Bury fans)