Spurs cruised into the semi-finals with a 3-0 win at Swansea with Christian Eriksen scoring twice to make light of Harry Kane's absence through injury.
But that didn't prevent Pochettino from criticising the use of technology as a lengthy delay followed a decision to rule out a Son Heung-Min strike for offside with Spurs leading 1-0.
"It’s a nightmare. I feel so sorry for the people trying to use that system," said Pochettino.
"I think I prefer it when the ref and assistant make mistakes than to wait three or four minutes for things."
Spurs have had to cope with more VAR controversy than most sides in England as their 6-1 5th round replay over Rochdale was littered with controversial video reviews.
On Friday, FIFA president Gianni Infantino gave the official green light for VAR to be used at the World Cup despite lingering doubts over its implementation.
The technology has been used widely in leading European leagues in Germany and Italy this season, but has been limited to a series of trials in Cup games in England.
"We now need to see the reality of how it is going to affect the staff on the touchline and the officials," added Pochettino.
“It is so complex, but the worst thing for me is the effect for the fan. It is going to be a massive problem for the future.
“We will see what happens at the World Cup."
Victory in Wales moved Spurs to within two games of capping an impressive four years of progress under Pochettino with a first trophy since 2008.
And both the semi-final and possible final will be at the club’s temporary home Wembley, where Spurs have lost just three of 24 games this season.
That record contrasts sharply with Tottenham's record at the national stadium last season, where they lost 4-2 to Chelsea in the FA Cup semi-finals and to Bayer Leverkusen and Monaco in the Champions League.
And Pochettino now believes home comforts could give Spurs an upper hand.
“Seven months ago, everyone said playing there at Wembley horrendous," said Pochettino.
"That was the feeling and the perception, but it has changed. We feel comfortable there and so do the fans.”
Eriksen took his tally to eight goals in 10 games against Swansea as he struck twice from outside the box either side of just Erik Lamela's second goal in 18 injury-ravaged months.
"Eriksen was fantastic, so important for us," added Pochettino.
"Every season he takes one step up, today he was fantastic. He is so consistent.”
Swansea had lost just twice in 15 previous games since Carlos Carvalhal's arrival as manager.
But the Portuguese had no complaints after seeing his side outclassed.
"I am not disappointed as they have a very good side," said Carvalhal, who took Swansea to the last eight for the first time since 1964.
"I said before to achieve something, we must be at our best and they must be not so good. We know there is a gap and that they are better."