The Irons, who last won against Chelsea on December 1, went ahead through a Mark Noble penalty after just three minutes when referee Mark Clattenburg spotted a shirt pull by defender Ryan Bennett on Winston Reid.
Robert Snodgrass later posted a Tweet claiming "the referee kills the game . #gamesgone", and while accepting there was cause for a foul, Hughton felt the penalty award was soft, as well as highlighting other calls which went against the visitors.
"The key decisions in the game did not go in our favour, but we did not start well enough," said Hughton, who confronted Clattenburg as he left the pitch at both half-time and following the full-time whistle.
"We accept Ryan Bennett had hold of the lad's shirt, but I also saw Reid's forearm in Ryan's chest. They are very close, he is not pulling Reid so he cannot get away, it is something you see game in and game out right throughout the country.
"On almost every occasion you do not see a penalty, particularly when it is so early in the game, so I was very surprised when he gave it.
"I also don't accept it was not a foul on Alex Tettey leading up to the second goal and certainly was a handball in the first half and then the incident on Harry Kane.
"We have been on the end of poor decisions today."