Although he didn't have a clear view, Mr Penn acted on the advice of one of his assistants who was on the far side of the pitch from the incident.
But the ref, who is in his first year on the league list, has now altered his view after watching it on video.
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While it didn't affect the outcome of the game, Latics now hope the yellow card shown to Filan for the challenge will be rescinded.
There is no right of appeal by the club, but the referee can mention it in the report he sends to the Football League and FA.
Manager Paul Jewell was outraged by the penalty decision and confronted Mr Penn at the final whistle – but not before steering a still-angry Filan away.
But he is pleased the ref agreed to watch the video and has been brave enough to change his mind.
Jewell said: "The referee rang me up to apologise for the penalty, and fair play to him for doing that.
"He told me he has now seen the video of the game and it wasn't a penalty.
"I had asked him at the end of the game to look at, and while it would have been nice to keep a clean sheet, at least it didn't cost us.
"I'm having a word with our chief executive Brenda Spencer to see whether we can get John's booking rescinded.
"We'll have to see what the referee says in his report, although I think he booked him for the challenge rather than dissent – it was Jason de Vos who got booked for dissent."
Jewell and chief scout David Hamilton were hitting the road today to watch Saturday's opponents Swindon Town in action against Blackpool at the County Ground.
And the boss believes Latics face a stern test in Wiltshire at the weekend.
He said: "They started the season well, hit something of a bad patch, but they have come through that.
* Latics are hosting their first Ladies Day when Cheltenham Town visit the JJB Stadium on February 1.
A bucks fizz reception, carvery lunch, executive match seats and a cocktail hour are all included in the package which costs £35 plus VAT or £25 plus VAT for season ticket holders.
More details from Jill Gregory on 01942 770 448.
* The away game at Crewe on February 15 has been made all-ticket, and seats went on sale to season ticket holders this morning (one per person).
Any remaining tickets will go on general sale on Monday, February 3.
Seats in the Blue Bell BMW Stand which runs down the side of the Gresty Road pitch cost £16 adults, £13 Over 60s, and £4 Under 16s.
Article from the Wigan Evening Post.