Sky Blues sub Max Biamou struck in injury time to give his side a victory which keeps them two points behind the top two.
Wanderers conceded a sloppy opener to Amadou Bakayoko but battled back after a largely forgettable first half to level through Dennis Politic.
The winger netted for the fifth time this season after turning in Chris O’Grady’s cross and it looked as if Bolton might go on to nick it – Daryl Murphy and Brandon Fleming both going close in the final few minutes.
Seven minutes of injury time was added on thanks to a clash of heads between Toto Nsiala and Callum O’Hare – the Wanderers man eventually forced off the pitch on advice from the medical staff.
But Biamou’s late goal left Bolton empty-handed and Hill feeling disconsolate.
“I thought we were unlucky,” he said. “I am really disappointed for the players.
“We got an excellent victory last week and we were the better side. Coming into this game we knew Coventry were a very good team knocking on the door of automatic places for promotion. It was a difficult ask and we didn’t get any rhythm, get close to them early on.
“The way we conceded the first goal is really poor but we weathered the storm. We grew into the first half and I thought we finished it well. And we competed well second half.
“After getting that equaliser we shot ourselves in the foot and I just feel sorry for the players because they deserved more against a good side, instead of knowing we deserved to get beat. We should have walked away from here with a point.”
Wanderers improved dramatically in the second half – something which provided Hill with some solace.
“It’s encouraging because we have a good group of players but we’re not the finished product,” he said.
“We are a long way from chasing Coventry down. On a 400m track they are 150 ahead of us with respect to building processes and getting a team on the pitch.
“There was a lot of effort on display, they tried matching up, but moments of composure and when you need to be better we just weren’t on the same par. It’s no disrespect, I’m disappointed they didn’t get a draw.”
On Ronan Darcy, who was absent from the matchday squad, Hill also revealed: “He is injured.
“He had an x-ray yesterday but I think he has been given the all-clear. It’s a foot injury.
“The x-ray proved there was no fracture, so we’re okay with that one. Sonny Graham was injured too.
“I don’t know if they will be back on the training pitch before Tuesday or not, we’ll have to wait and see.”