Twice in the final few minutes of the game in Budapest, Savs clashed with opposing defender Zoltan Peto and then at the final whistle was involved in an argument with Hungarian coach Lothar Matthaus.
However, Hughes played down the confrontation although he claimed that some of the Welsh side had complained at being spat at throughout the ill-tempered 'friendly' international.
"I did not think Robbie did anything wrong," said the Wales boss.
"Maybe Lothar hasn't seen Robbie Savage perform before, he was competitive, but Lothar knows about him now.
"Frankly what happened at the end was something and nothing.
"Hungary completely lost their discipline towards the end of the game and my players kept their nerve really well. When you see people spitting at fellow professionals that's an absolute disgrace," he added.
"We play them again in February so we hope that doesn't happen again."