The result leaves City 11 points behind leaders Liverpool.
Stones lamented, “It's a difficult one to take, conceding so late, having scored so late. It was one of those games.
“They set out the gameplan quite early – five at the back, 11 men behind. We kept pushing, trying to break them down.
“Teams know how we play and they've got to find a way to try and stop us. That's them showing us respect.
“We have to figure it out, use our flair and how we play. We train every day to break down these systems.
“I thought we did that really well and created some great chances.
“We got our break in the first half and conceded two sloppy goals.
“We switched off in key moments. We played some unbelievable football and took as many shots as we could. It's frustrating.
“We could have taken our chances and the game could have been over. All of us needed to chip in and do a part for the team.
“In the individual actions and team actions in the late stages, that's what cost us the three points."