Tottenham had an early goal disallowed by the VAR, who then awarded it a penalty in its fifth-round replay at a snowy Wembley Stadium.
That spot-kick was converted by Son Heung-min, only for referee Paul Tierney to chalk off his effort and book the player for stopping during his run-up, leaving the match balanced at 1-1 at halftime with emotions on the pitch running high.
"It was so complicated because of the new system. It was difficult to keep focus on the game," Pochettino said.
"I told the players to keep focused at halftime. The circumstances were difficult. I think we have the best referees in Europe or the world but I don't know if this system will help them or cause more confusion.
"It is a game of emotion. If we are going to kill this emotion, I think we are going to change the game."
The FA Cup is one of several competitions around the world that are trialling the system this season.
"I feel so sorry for the referee and more, I feel sorry for the fans, because it's so difficult to understand the situation," Pochettino said
