Leon Clarke's first league goal for the Sky Blues proved decisive and left Rovers ahead of Doncaster only on goal difference, and having played a game more.
Despite a poor first-half showing when utilising a pacy three-man attack, Moore felt his team were worthy of a share of the spoils.
"I think without doubt we should have got a point," he said. "I thought we were poor in the first half. I thought Coventry bossed it.
"We tried to change it a little bit with three players up front who can catch pigeons. We never got going but then credit to them in the second half, we gave it a go.
"One of our bigger lads got done with the header at the corner and Clarke did what he is good at and scored from the knock-back.
"It was always going to be a tough game. When you look at it, Tranmere are coming here and are disappointed we have lost.
"When we got the ball we didn't exploit their lack of pace at the back in the first half. We played better in the second half when we went back to 4-4-2 but we need to be adaptable."