The Reds were beaten on their travels despite tries from Kyle Adams and Jack Hamilton, adding to a penalty try forced by the Reds’ set-piece dominance.
And Welshman Thomas was disappointed after his charges slumped to consecutive league defeats, all-but ending their promotion hopes.
He said after the match: “We travelled with a strong squad and were confident we could come away with a win against a side that has been struggling in the league.
“We started brightly and for the first 10 minutes we looked in control and well organised but we weren’t able to maintain this for the duration of the game.”
The first of Haddington’s three tries came from flying winger Adams, who intercepted an Irvine pass to sprint clear of the covering defenders to score.
Jack Hamilton was at his livewire best to snipe over from close range for their second, and a penalty try brought the Reds their third of the day.
Gareth Pritchard, once more at stand-off, added all three conversions, but the Neilson Park outfit returned with only a bonus point – earned as they finished within seven points of the victors.
Thomas added: “Although we had opportunities to win the game we fell short and had to settle for a losing bonus point.
“We set ourselves high standards that we unfortunately fell short of this week.
“We are all keen to get back training to work on things and prepare for the remaining games of what has been a very positive league campaign.”
The Reds were due to take on GHK this weekend, but the league leaders’ involvement in the BT Cup means that match has been postponed.
Haddington: J Ferguson, K Adams, I Watt, L Clutton, M Robertson; G Pritchard, J Hamilton; M Dunlop, C Stuart, P Smith, B Laing, H Hamilton, C Hamilton, J Riddell, M Renton.