The Sky Blues were toothless and sloppy in the first 45 minutes and were lucky not to be further down than a single goal when the referee blew the whistle for the half-time break.
However, Vitezslav Lavicka's men rallied in the second term and were far more dangerous in going forward but couldn't quite the bridge the gap with the A-League leaders who were much more adept at retaining the ball.
"In the first half we didn't keep possession well enough, especially against a team like Roar who like to keep possession," said McFlynn.
"That was what we did a lot better in the second half - kept the ball a lot more, created a few chances but in the end it wasn't enough. We defended well but we just didn't keep possession enough."
With the season now beginning to get away from the reigning champions, who now sit 9th on the table on just 18 points from 19 matches, McFlynn was maintaining a defiant approach.
"We've got strong characters in the group, we never give up. We're still within touching distance of the finals and the good thing about football is there is always a game quick and fast to get three points and luckily for us that's this Wednesday night, so we'll be focusing on getting the three points up there," McFlynn added.