Fernando Llorente struck a perfect hat-trick in a 6-1 rout of the League One side at a snowy Wembley on Wednesday to book a quarter-final meeting with Swansea City.
But the headlines were made by VAR yet again, with the technology being trialled in English football for the first time in the FA Cup.
Referee Paul Tierney consulted VAR before ruling out Erik Lamela's fifth-minute effort, while Spurs were then awarded a penalty thanks to the system.
However, the subsequent strike was disallowed by the official following yet another lengthy review after Son Heung-min feinted in his run-up.
Fans and pundits alike were left confused by the use of the technology and Pochettino said it was difficult for his players to concentrate during an eventful first half, with the score 1-1 at the break before Spurs pulled away after the interval.
"It was a game we can talk about different things," Pochettino 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 told 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.
"We have a tough game at Swansea and we will have a competitive time."
Having pegged Spurs back for the second time this month before the Premier League side's class told after the interval, Dale boss Keith Hill was thrilled with the way his team competed.
"The first half was special," Hill told BBC Sport. "Tottenham are a marvellous and exceptional side and I hope they go on to win the FA Cup.
"In no shape or form am I embarrassed about the way they [Rochdale players] took them on. Let's be proud about what we tried to achieve.
"It's not often you get an opportunity to pit your wits against a special side. We will miss it this week but we look forward to the league games."