The Manchester City manager was seen berating the fourth official, Craig Pawson as the first half ended.
It's unclear why Guardiola was so irritated, but his side had just been pegged back in the second minute of added time following Elijah Adebayo's goal.
Fancy footwork from Ross Barkley in the middle allowed Alfie Doughty to plough forward before passing to Andros Townsend.
The former Everton man's cross from the right landed was pinged perfectly onto Adebayo's head at the far post, as he rose to fire it into the back of Ederson's net.
But whilst Hatters fans went wild inside Kenilworth Road as the whistle blew for half-time, Guardiola's face told a different story.
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The City boss was seen in deep conversation with Pawson, even pointing a finger at him at one point as they headed for the tunnel.
Man City had been on an uncharacteristically poor run, with the reigning Premier League champions winless in four in the league.
Man City lost 1-0 to Aston Villa on Wednesday, drew 3-3 with Tottenham, 1-1 with Liverpool and 4-4 with Chelsea.
Indeed, Sunday's game saw them fall 1-0 behind in three successive Premier League games for the first time since November 2019.
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That was the last season they failed to win the title, with Liverpool clinching it instead.
City were also missing star striker Erling Haaland, with Guardiola revealing the Norwegian was absent for Sunday's clash due to injury.
However, the Citizens went 2-1 quickly after the break, with Bernardo Silva finding the net before Jack Grealish scored his 50th career goal and seal all the three points.
Man City remain in fourth, four points off leaders Liverpool, whilst Luton stay in the relegation zone, four points off safety.