Erik Lamela thought that he had given Spurs an early lead in the fifth-round encounter, only for his goal to be ruled out for a foul in the build-up after a lengthy consultation between referee Paul Tierney and his video assistant.
Tottenham were then awarded a free kick when Kieran Trippier was fouled, only for Tierney to point to the penalty spot after another VAR ruling.
Spurs ran out comfortable 6-1 winners in the end, with Fernando Llorente bagging a hat-trick alongside a Son brace and an injury-time addition by Kyle Walker-Peters, but Pochettino was left bemused at the VAR controversy.
"It was a game we can talk about different things," the Argentine told BBC Sport. "It was so complicated because of the new system, it was difficult to keep focus on the game. The job is done and we are happy because we are in a quarter-final.
"I took the players to keep focused at half-time. 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.
"It's difficult for the referee - I feel so sorry for the referee and more I feel sorry for the fans because it's so difficult to understand the situation."
Spurs go on to face Swansea City in the quarter-finals of the FA Cup.