Early in the teams' Champions League quarter-final first leg, Danny Rose was called for a penalty after blocking Raheem Sterling's shot with his arm.
Bjorn Kuipers awarded the spot-kick following a lengthy review, with many disagreeing that Rose had done enough to warrant a foul being called.
And the Tottenham boss was among that group, saying that the call showed that VAR causes more problems than it is solving.
"I think that today proves that VAR has a lot of work to do between us, between the referees, the fans and the players," Pochettino told beIN SPORTS.
"It's a situation that we need to check the protocol and be clear.
"Today was a clear example that rather than helping, it's causing more problems.
"You can accept when a decision comes from the referee and it's a mistake.
"A decision like this is going to be difficult. I want to help VAR but I think we need to work a lot to develop it and help the referee to make better decisions."
Tottenham ultimately did not have to pay the price for Rose's penalty, as Hugo Lloris saved Sergio Aguero's ensuing spot-kick to keep the game tied 0-0.
That provided an opening for Son Heung-Min, whose 78th-minute goal gave Spurs a 1-0 advantage heading into next Wednesday's second leg at the Etihad Stadium.
Pochettino was pleased with the result and Son's goal, but still insisted that City were the favourites to progress to the semi-finals.
"Amazing, very good, happy for him," Pochettino said of Son.
"I think the team deserved the victory but there is still work to do.
"Manchester City are still the favourites but the victory makes us believe a little bit more."
Spurs return to the pitch against Huddersfield on Saturday as they turn their attention back to the Premier League briefly ahead of next week’s second leg against City.