The Saddlers went ahead in the 13th minute thanks to Danny Johnson's early strike - his fifth goal of the campaign.
Johnson and Andy Williams both had second half chances to kill off the game - before Danny Rose headed home with virtually the last act of the game to rescue a point for Steve Evans' side.
The referee had indicated eight minutes of added time to the bemusement of many in the ground - before going on to play more than 100.
But although he believed the ten added minutes were excessive - the Saddlers boss said he looks at his own side first and believes they should have had the three points in the bag earlier.
He said: "It is frustrating that eight go up and we play over 100 minutes, but we still have to switch on and do our jobs.
"There were one or two errors at the back when that ball comes in but we should have killed the game off, we had the chances to kill the game off.
"When you've been around football a long time if you don't kill the opposition off they still have that breath and belief inthem to keep going and that is what Stevenage did, they have got a lot of late goals this season, so I am going to have to credit them on that as well.
"Owen Evans made one great save in the first half and that was the only real opportunity they had, like I said we should have killed it off.
"I always look at ourselves in the first instance and how we can be better it was the wrong choices in key moments and we didn't get the second goal.
"Once we would have got the second goal then that would have been the three points done and dusted.
"But it wasn't to be, we're still unbeaten and we go on to Tuesday which is going to be a tough game."
Although frustrated at the time added on Flynn didn't speak to the referee after the game - and added his side will learn lessons from their late heart break.
He added: "No I didn't have a word with the ref, we know it shouldn't have been ten, maybe nine, because they say it is a minimum of eight.
"But maybe nine, but the extra minute and a half that was added on shouldn't have been.
"But we should syill see that game off, it was the last ten seconds of a game, and we have to be a bit switched more on those occasions.
"And we have been to be honest, only conceding one goal in four games shows us we have been, so it is frustrating but we will move on a learn from it."