The Welshman felt his side controlled the game and was happy with his players' performance at Craven Cottage despite falling to defeat thanks to Darren Bent's goal
The Welshman felt his should have been given two penalties in the first half, while he also suggested that Pajtim Kasami should have been sent off for appearing to slap Erik Pieters.
However, neither of the decisions were given Stoke’s way and a late goal by Darren Bent ensured the Potters were left empty-handed at Craven Cottage.
"We should have had two penalties and [Pajtim] Kasami should have been sent off because he raised his hands," Hughes said in his post-match press conference.
"Those were key moments that shaped the game and the outcome of the game. Unfortunately, it affected us in a negative way. Obviously, given the time of those incidents, they would have swung the game totally in our direction.
"If you raise your hands, it’s a sending off. The fourth official, I spoke to him, and he said there was contact outside the box [for the penalty decision]. As the guy’s fallen, he’s fallen on the back of Jon’s [Walters] heels, so he’s obviously impeded him. I didn’t understand it at all."
The 49-year-old also felt his side dominated the game and looked likelier than Fulham to register a late winner.
"I think that’s the top or bottom if it," he continued. "The team that was most likely to win the game, I thought that was us. I thought we controlled the game, trying to create opportunities for ourselves.
"I thought we did that and had good opportunities to pick the right pass and I thought we did it. I thought we were more likely to win the game and I think they’ll agree they were a little bit fortunate."
Hughes also refuted any extra significance to Saturday’s result due to his decision to leave Fulham in 2011, going on to suggest that he is happy with his side’s overall form.
"Today was an opportunity to get maximum points because I felt we were the better team," he added. "I wasn’t trying to points score today [as former manager]. Over the course of the 90 minutes, I thought we were the better team.
"Last weekend, we were disappointed with what we produced against Norwich but I wasn’t disappointed with the performance today.
"I’ve been more than happy with what we’ve been producing. The end product is obviously something we need to address."