The Saddlers are nine without victory across all competitions having been downed 1-0 by the League Two leaders at Brisbane Road.
Flynn's men enjoyed a solid first half but failed to replicate that performance level in the second period, with Omar Beckles' close-range finish sealing it for the hosts.
"They scuffed the ball in from three yards and we had four players around him. We've let a runner go," said Flynn.
"It's probably the only time we switched off apart from right at the beginning where we nearly did a carbon copy of the goal we gave away against Colchester.
"Those were the only times they really cut us open or got in behind us.
"In the second half, we weren't good enough with the ball. We lost too many first and second balls.
"Although we looked quite solid, we weren't good enough with the ball.
"Even in the first half, I thought we played well, but it was the final ball. We lacked quality in the final third – not getting past the first man with our crosses. It was just huffing and puffing.
"We weren't really poor in the second half. We just weren't good enough with the ball and didn't win enough individual battles.
"They're the league leaders full of confidence, with probably a fully-fit squad, and we've got nine missing.
"I'm not going to get too down about it, but we need to start winning."
Walsall were without Tom Knowles following his goal in the draw against Colchester United as he has been struggling with a sickness bug.
Hayden White (head) and Douglas James-Taylor (back) also missed out with knocks while Flynn named just six substitutes.
The Saddlers are now 15th in the table with nine points from nine games.
"If we come away with a 0-0, it's the perfect performance, really, considering the amount we've got missing," added Flynn.
"It is what it is. We're down on our luck at the minute, and we need it to turn."