Glendale (11-3-8) cut the lead in half roughly five minutes before intermission when junior forward Alan Ghazarians blasted a shot that was saved but fumbled. Junior midfielder Kelby Hernandez followed the play in and booted in the rebound.
The true turning point, according to Marroquin, came in the second half when Bonita was awarded a penalty kick and converted for a 3-1 lead.
"It was a stupid call," said Marroquin, whose team tied for third in the Pacific League. "We were in it up to that point. We were attacking and they were going back and forth, back and forth.
"We still got a few shots after that, but nothing on frame."
Though both teams had to deal with the elements, Marroquin said his squad seemed to have a tougher time dealing with the rain.
"The rain played a part," he said. "[Bonita] adjusted a lot quicker."
The game was the third in a row for the Nitros without senior forward Levon Sargsyan, the team's leading scorer. Having dealt with that shortcoming and still having fared far better than last year's playoff showing, Marroquin was happy with his team's season.
"I'm happy with the guys," said Marroquin, whose team was defeated by Rio Mesa, 6-0, last season and collected a 2-2 (5-4) wild-card win over Culver City in a wild-card match on Wednesday before Friday's close loss. "They never quit, they kept fighting through it.
"Our goal is to get better each year and we're doing that."