The Gypsy King retained his WBC heavyweight title by beating the Bronze Bomber via knockout in the 11th round.
However, Wilder had his moments throughout the bout and knocked Fury down twice in the fourth round.
On both occasions, the Brit got up but it appeared that referee Russell Mora gave him a long count.
The reason behind this was because he stopped counting for a couple of seconds when he asked Wilder to go towards a neutral corner.
However, Rogan claimed that the counting should not have stopped and that Fury benefited from it.
Joe Rogan has his say on 'long count' controversy
He said: "This is what happened. The referee is supposed to go ‘One two…’ when the guy goes down. But if for any reason he has to interrupt the count… you’re supposed to pick up the count where the ringside counter has it.
"So there’s a guy who’s counting ringside, and he’ll keep the count going. So if you’re at ‘One, two,’ and then you’re like ‘Go to a neutral corner,’ that guy is supposed to be like ‘three, four, five,’ but he didn’t.
"He went back to it, ‘three, four,’ but the guy had already been down for a couple seconds. Without a doubt it was a long count.
I think it’s an error, or corruption. Most likely an error, most likely the guy’s panicking.
Wilder will definitely agree with Rogan's comments and expect him to say "this is also how I was robbed in the first fight."
During their first encounter, he knocked Fury down during the final round but he came up. The fight ended in a draw but Wilder still considers it as a knockout.
It will be interesting to see what's next for both fighters. There is a good chance of Fury facing Dillian Whyte if the latter defeats Otto Wallin.