Half-time substitute Max Kretzschmar scored twice to give Wycombe a 2-1 win at Victoria Park and leave Pools winless this season after six games in Sky Bet League Two.
Substitute James Poole headed in from close range in injury time to score Hartlepool's first league goal of the season but it was too little, too late for the hosts.
Cooper, whose side beat Bradford 5-0 in the Football League Trophy in midweek, was frustrated.
He said: "The first goal was vital. It proves the case with us.
"The instruction was to start the second half at a high-tempo and put Wycombe on the back foot and it didn't happen
"The two goals they scored weren't good goals, but enough to give them the points.
"The whole place felt flat - the players, the crowd. There was a slow tempo with the referee, even though I asked for it to be speeded up throughout. It gets frustrating.
"I felt the officials were allowing Wycombe to slow the game down and not allow us to get into any tempo.
"The start to the second half wasn't in any way, shape or form what I expect."
"Loads of huffs and puffs and knock-downs and it didn't fall for us like it did the other night. We look at reasons why."