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Kofi Balmer is free to face Hearts on Saturday after Motherwell successfully appealed against the defender's red card at Kilmarnock.
Well say they "are delighted that the correct decision has eventually been reached" but cited "concerns".
Balmer, 24, was sent off when he caught Killie's Fraser Murray following a clearance on Saturday. The incident happened while Well were a goal down and they would eventually lose 2-0.
Referee Matthew MacDermid did not initially show a red but VAR Andrew Dallas instructed the on-field official to review the tackle.
"This is the second time this season the club has had to go through the time, effort and expenditure to appeal a red card decision," Motherwell said.
"We have concerns that VAR felt that this was an obvious refereeing error in the first place. Again, the on-field review has come out with the wrong outcome.
"We spend a significant six-figure sum each season towards the running costs of VAR at the stadium.
"There have been eight instances so far this season where Motherwell have been directly impacted by what has subsequently been deemed an incorrect referee or VAR decision."
The Fir Park club fear "continued errors throughout the season, for all clubs, will have a direct impact on where teams will finish in the final standings, which obviously determines finances for each club".
And their statement concluded: "We hope that with the financial commitment put on the club to use VAR, combined with the frustration our fans get from the game due to the intervention from VAR, we see significant improvement in its implementation going forward."
Hearts visit Michael Wimmer's Motherwell on Saturday in the final round of fixtures before the Scottish Premiership split, with both clubs and St Mirren in contention to take up the final top-six place available.