Julen Lopetegui says Wolverhampton Wanderers have written to the Football Association asking it to explain the circumstances surrounding Toti Gomes' disallowed goal against Liverpool.
The video assistant referee (VAR) had no camera angle available to provide any evidence to overturn the decision.
"It's very clear something has happened." said Lopetegui.
"Of course I have seen the images on the internet. I have my opinion, we have sent our comments and we are waiting for an explanation."
The FA Cup third-round tie at Anfield ended 2-2.
Wolves were also unhappy that Mohamed Salah's goal, which put Liverpool 2-1 ahead, was allowed to stand, despite the Egypt forward appearing to be in an offside position when the ball was played to him during the build-up.
Speaking after the game on Saturday night, Lopetegui, who went into referee Andrew Madley's room with captain Ruben Neves after the game, said the offside "doesn't exist" and that it was a "pity" because his players "deserved to pass to the next round".
The Wolves Trust, a supporters' group, also released a statement demanding answers and an apology from the FA or referees' body Professional Game Match Officials Limited (PGMOL).
"The FA Cup tie at Anfield was effectively decided by a linesman error and VAR technology failure. How does this occur at a stadium regularly hosting Champions League matches and professionally trained match officials?" read the statement.
"We await a statement from the FA or PGMOL, explaining exactly what happened but also offering travelling Wolves supporters an apology.
"Only by messaging family and friends watching on TV were those in the stadium able to get an idea as to what was going on; not only is this wrong but it undermines the credibility of the game."
The replay at Molineux has been scheduled for Tuesday 17 January at 19:45 GMT.