The decision proved costly for Cooper as Matt McClure gave Wycombe's survival hopes a massive boost as he scored a header in the second half to take all three points.
Jack Barmby had earlier given play-off chasing Hartlepool the lead before the break but Wycombe came from behind thanks to second-half goals from Dean Morgan and McClure.
Cooper said: "The referee said there was contact but that it's a coming together.
"Who knows exactly what happened. He got bundled from behind and lost his footing.
"The defender's trying to get back and he can't get goal side of Luke. He's putting him under pressure from behind to try and avoid Luke from getting a shot off but he's bundled him over.
"It's a penalty and a red-card. We can't do anything about it because he hasn't given it. Why can he give decisions all over the pitch but not make the big ones? It baffles me but I can't do much about it.
"I've had a word with the referee to have a look because we believe we've been harshly treated.
"I know for a fact that if I went into the referee's office half an hour after the game that the answers would be ready so I'm not going to do that. I've done it twice this season and it becomes a pointless exercise."
With just four minutes played, Hartlepool's top goal scorer James found himself through on goal but his calls for a penalty were waved away.
With Wycombe applying all the pressure, Gareth Ainsworth's men were leaving themselves open and it was Manchester United loanee Barmby that put the visitors ahead at the break when his effort lofted over Matt Ingram.
Wycombe seemed unaffected by the goal and grabbed a deserved equaliser within five minutes of the restart when Morgan headed in his seventh league goal of the season.
With 20 minutes remaining, substitute McClure put the Chairboys ahead when he headed in a drilled corner from Kretzschmar to score his seventh goal.
Pools were pushing for the equaliser and Cooper's side had Scott Flinders to thank for staying in the game when the keeper tipped over McClure's effort from the edge of the box.
- Sports & Recreation
- Matt McClure
- Dean Morgan
- Jack Barmby