The Saddlers were denied what appeared to be a stonewall penalty as Jack Earing was wiped out by Cheltenham Town keeper Shaun MacDonald in Tuesday night’s 2-1 Papa John’s Trophy loss.
Flynn also bemoaned the standard of refereeing last month when Andy Williams had a goal chalked off in their Carabao Cup loss to Charlton Athletic – a chested finish deemed to be a handball and Williams booked.
The Walsall chief opted to speak to the EFL’s head of refereeing Mike Jones after Tuesday’s loss but felt he did not gain much from the conversation.
“I usually leave them alone, but I did ring the head of referees on Wednesday,” said Flynn.
“I won’t be doing it again. It’s a waste of time. I actually like Mike Jones. He’s a fairly decent bloke from the times I’ve met him, but I won’t be ringing him again.”
Flynn continued: “I’ve spoken to other managers and we feel this is the worst standard of officials – up and down the country and not just in our league – that I’ve seen.
“You can go into a whole lot of different things. The lower levels aren’t full-time. There’s no real consequences on it. OK, they might miss a game (after a bad decision).
“At the higher level, I don’t know how they get some things they get wrong with the VAR.
“It’s not a question for me. Maybe they need to get more people in who understand the game.
“It’s hard. You’ve got Mike Dean who’s been a Premier League referee and is now head of the VAR.
“How are they looking at it? Until I know how they’re seeing the game, I can’t give you an educated answer. I don’t know, but I do know the standard is getting worse.”
Flynn also acknowledged his side’s shortcomings and has urged them to stop conceding goals in quick succession.
“There’s been a bit too much for my liking where we’ve conceded the first one, and then conceded the second within five to six minutes,” he added.
“If players are switching off or letting the disappointment of conceding the first one get to them, we’ve got to cut that out.
“I’m looking at everything and we’ve got stop one becoming two like it has.”