The Tottenham boss admits the midfielder could have been sent off against Arsenal.
However, the Argentine says the referee's decision is final - and believes the sending off of Francis Coquelin didn't actually affect the result.
Tottenham drew 2-2 with Arsenal after goals from Aaron Ramsey, Toby Alderweireld, Harry Kane and Alexis Sanchez meant the spoils were shared at White Hart Lane.
Pochettino told Sky: "I think that the sending off didn't affect the result. Maybe Dier could have had a second yellow, yes, but it's always down to the decision of the referee - they are the boss."
With both Spurs and the Gunners dropping points on Saturday, it's now time to look ahead for both.
Tottenham have Borussia Dortmund in the Europa League next Thursday, while Arsenal face Barcelona in the Champions League the following week.
In the league, though, Tottenham can look forward to a trip against Aston Villa. A win at Villa Park is the biggest banker in football right now.
Arsenal, meanwhile, travel to Hull City in the FA Cup on Tuesday night, before hosting West Brom in the Premier League next weekend.