Having fallen behind after just 55 seconds Gillingham came back strongly and deserved their equaliser when Cody McDonald latched onto a ball in the box and fired home.
"It's hard to take," he said. "The players put in a fantastic performance. We had a gameplan to frustrate them.
"I came here to watch Coventry play last Sunday and they were absolutely fantastic. There was no way that we could leave ourselves open - we couldn't do that.
"We did know the areas where they were weak and we exploited them and we had enough chances in the first half.
"They put their bodies on the line and to lose so close to the end from a corner, with the players we have in our squad is very disappointing.
"It was always going to be difficult but we knew they would be vulnerable on the counter attack. That was the way it had to be because we couldn't play and open, expansive game because they have great movement and highly technical players.
"If you'd sat with me last week and seen what that was like compared with this, you'd know we put in a good effort."