Stand-in manager Rob Page admitted Port Vale had been fortunate in their 1-1 draw against Bristol City.
The Robins dominated most of the game and a second-half goal by Scott Wagstaff looked set to earn them a first league win of the season.
But Aden Flint's dreadful back pass was pounced on by Vale substitute Hughes, who took the ball around Elliott Parish to net the 90th-minute leveller.
Page, who is in charge while Micky Adams recovers from hip replacement surgery, said: "Lee Hughes has been around a long time and been involved in a lot of big games. You have to give him a lot of credit for anticipating the mistake and then taking his chance.
"We put him on for the last 25 minutes and he has run around and given us everything. He's been there and done it and in that situation he has shown he will still put the ball in the net.
"I'm pleased with the point and we will take it, but we are not over the moon with the performance. We didn't do the ugly side of the game very well at all.
"Our game is to make things difficult for the opposition and grind them down, but that didn't happen. The positive was we didn't cave in and have escaped with a point.
"We will look at the video on Monday, assess what wasn't right and move on."