Ian Baraclough pointed a finger at the officials after Northern Ireland's late defeat to Austria in Vienna left them facing relegation in the Nations League.
After the cancellation of Romania's match against Norway, Northern Ireland needed a win to be sure of staying alive in the competition and an encouraging performance in the wake of Thursday's heart-breaking Euro 2020 play-off loss to Slovakia had them on course when Josh Magennis scored in the 75th minute.
But the lead lasted only six minutes, with more than a hint of offside to Louis Schaub's equaliser before Adrian Grbic completed the turnaround in the 87th minute.
"We took the lead with a good goal and I thought we were fully justified for it," Baraclough said.
"Then their first goal, I'm frustrated. I just looked back and the guy is offside. He's offside in the first phase and then in the second phase he's offside again and the officials haven't picked it up.
"That changes the whole outcome of the game for me.
"(Austria) have gone 1-0 down and, credit to them, they stepped it up and put pressure on us, but I don't think it ends up at 2-1 if that first goal is disallowed. It's hard to take for me and my team."
Despite the frustration, Baraclough said he was proud of his players' response to Thursday's extra-time loss at Windsor Park as a much-changed side held their own and frustrated the Group B1 leaders for long periods.
"I'm disappointed to come away having lost 2-1, especially when we've taken the lead," he said.
"This was a difficult game for us anyway, coming into the game after the disappointment of losing to Slovakia and working for 120 minutes.
"To then travel over here to play a game so quickly, I thought we were excellent in our shape, our set-up. We were compact, we made it difficult for Austria. Austria had to change their shape and that's a credit to our lads."
Baraclough and Northern Ireland must now await word from UEFA on how the Romania-Norway situation will be handled.
Romania are expected to be handed a walkover victory after Norway were unable to travel due to positive tests for coronavirus. If confirmed, that would leave Northern Ireland six points behind Romania before Wednesday's meeting between the sides at Windsor Park – the final game of the group.
UEFA's control, ethics and disciplinary body is due to discuss the matter at a meeting on Monday.
Stuart Dallas, captain on the night, said: "It's something we can't control. Whatever happens, happens. We find ourselves in this position because we haven't been able to pick up points early in the group.
"It's important we don't rely on anyone else and just put in a positive performance and try to get a win (on Wednesday).
"It's three or four months until we meet up again so it would certainty put us into a positive mood going into the World Cup campaign."
