Julen Lopetegui says Wolverhampton Wanderers have written to the Football Association asking it to explain the circumstances surrounding Toti Gomes' disallowed goal against Liverpool.
Toti's late strike was ruled out because Matheus Nunes had been flagged offside after taking a corner.
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.