After a positive first-half performance, The Reds were flat at the start of the second half and allowed Coventry a way back into the game before Lyle Taylor’s injury-time penalty secured the three points.
Speaking after the match, Hughton said: “It was very much a game of two halves. I thought we were good in the first half and my biggest disappointment, and that probably goes back to where we are in this moment, is that we had a lot of the ball in the final third but didn’t make the most of the possession that we had.
“We didn’t create enough shots at goal, really good opportunities or crosses for the possession that we had.
“I didn’t think we started the second half well which surprised me and we are up against a very well drilled Coventry side that have been together for some time.
“But it is a good feeling to get that win and we just have to take that onto the next game.”
The Reds took the lead in a game for the first time since Hughton’s first game as manager, and he had hoped the team would have kicked on from there.
But the second-half display left a lot to be desired but Hughton will take the last-gasp victory.
He said: “The feel should have been that we have gone in at half time 1-0 up, so there should have been that feel-good factor in the team. I think there was a combination of they started better than us and we didn’t start well.
“With that being the case, it took us a little while to get back into our stride and by then, they were in good momentum. Of course, when they got the goal, you might have thought that if one side would go on to win it, it might be them.
“We steadied it again and it looked like it was ebbing out to be a draw until that last moment.
“Whether we deserved to get something out of the game, I think we did, and whether we deserved the win or not, that is something different but we will certainly take it.”