The Saddlers' 2-1 loss at Cheltenham Town in the Papa John's Trophy has pretty much scuppered their chances of getting through Southern Group C.
The run without a victory in all competitions, meanwhile, now stands at 10 matches.
Walsall were denied what appeared to be a stonewall penalty early on before ultimately falling short at Whaddon Road.
"We're probably out of two cups now because of refereeing decisions," said Flynn.
"It was an exciting game. I was disappointed to go in 2-0 down at half-time.
"We could have folded, but that's not what teams of mine do.
"They keep going, keep working for each other.
"When things aren't going your way, the only way you get out of it is by working harder and harder.
"I was very pleased with what I saw (in that respect).
"We've got to dust ourselves down, keep believing and make sure we stay positive."
The Saddlers were two down at half-time as Dan Nlundulu and Liam Sercombe struck for the hosts.
Before that, Jack Earing was wiped out by Shaun McDonald for what seemed a sure-fire spot-kick.
It was bizarrely waved away, though, while a few other penalty appeals were ignored.
Danny Johnson's late reply for Walsall was then too little too late.
"We could've had four penalties, by the way," added Flynn.
"Peter Clarke had his shirt ripped off in the box. Jack Earing has been bowled over twice.
"I've never been involved in so many stonewall penalty incidents and not got one."