Davinson Sanchez was proving to be a threat in the air from set pieces, but the Colombia worldwide did not make the most of a headed chance just before the break.
Pochettino's side had taken the lead just after the restart when Abdoulaye Doucoure turned into his own net, but the Hornets surged back and took all three points through headers by Troy Deeney and Craig Cathcart.
"It is so painful to concede two goals like this", Pochettino said.
However, Mauricio Pochettino has warned his players not to get ahead of themselves as they still have a lot of work to do to prove they are ready to challenge the likes of Manchester City and Liverpool for the title this season. If you want to be a contender - I am the first person guilty of everything - it is so hard to understand, because I thought we controlled the game in the first 45 minutes.
It remains to be seen how long Javi Gracia's third-placed side can remain among the upper echelon, but this win confirmed they are now there on merit.
Watford have also enjoyed an excellent start to the season as Javi Garcia's men sit level with Tottenham on nine points having won their opening three matches against Brighton, Burnley and Crystal Palace so someone's ideal record has to go tomorrow. We conceded two goals that if you want to be a contender, you can not concede.
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"The second half we scored and then they showed more strength (and were) more aggressive in the situation".
"I am not really interested in records but I am happy for the boys, for the team and for the whole club that we won today".
"We need to show more respect to this competition". You need to show respect because to compete to win it is not easy. 'But I always think we can do more.
"It's about energy and communication". "But the last three wins, when we won games, nobody asked me [about that]". "For us we are a little bit in the shadow".
Pochettino followed that up after the defeat to Watford by saying: "In the week I was trying to explain to the players we weren't as great as the perception".