The Saddlers looked to be heading for three wins from the first three games before Danny Rose netted a 100th-minute equaliser.
It came after Walsall had squandered a handful of second-half chances, with Flynn insisting they let the visitors off the hook – something he is keen to avoid again.
“They came with a game plan, it was not pretty but it was effective, and we should have seen it out, that is the frustrating thing for me,” explained Flynn.
“There was lots we can improve on. We let them off the hook, because when we played, we looked by far the better team.
“But we didn’t do it enough, or do it with enough quality.
“I am sure there will be times when we score late and get something we didn’t deserve, or something we do deserve.
“It is what it is, We will analyse Barrow now and see where we can improve.”
The Walsall boss also addressed the potential for any new signings to come through the door - after co-chairman Leigh Pomlett said the club could still make one or two new signings.
Flynn, who has so far signed 16 new players in what has been a busy summer at the Bescot, said: “We’ve got nothing ongoing at the moment, but we are still looking.”