Dave Jones felt his young team were "mugged" by play-off chasing Wycombe Wanderers who ended Hartlepool United's five-match unbeaten run at the Northern Gas & Power Stadium.
Wycombe's bulldozer of a forward, Adebayo Akinfenwa, stroked home the first in the 24th minute with sub Paris Cowan-Hall adding the second in the final minute of the 90.
In between, Pools rarely got going and had just one effort on target when Jamal Blackman saved Scott Harrison's header from Lewis Alessandra's corner.
Otherwise, the hosts huffed and puffed at times but did not threaten the away goal.
"We got mugged by a far more experienced side than us," said Jones.
"We've attacked and attacked, played well, we just lacked that bit of quality in the final third."
Pools had two strong first-half penalty appeals turned down by referee Dave Webb, either side of Akinfenwa's goal.
The hosts had their first shout in the 22nd minute when Thomas hit the deck in the box after a rapid Pools counter-attack led by Lewis Alessandra.
Mr Webb rejected the attacker's passionate pleas and then repeated the trick when there appeared to be a handball in a scramble following a 36th-minute corner.
Jones was seen in animated discussion with fourth official Shaun Hudson at the Pools dug-out.
"There were things going on I didn't agree with," he said. "Me and the fourth official were seeing a totally different game.
"It [the Thomas incident] was a penalty, of course it was."
Jones was not as vehement over the handball cries but for all the crowd frustration over the referee's handling of the match, the manager refused to blame the Co Durham official.
"I don't think it cost us the game," he added. “We missed a bit of nous."