The Toffees took the lead against the reigning Premier League champions through Marouane Fellaini before the Belgian gave a spot-kick away for a pull on Edin Dzeko.
But the England centre-back believes the tussle was nothing out of the ordinary, and insisted his side were unfortunate.
"We're pleased but a little bit frustrated," he told the club's official website. "We played really well in the first half, stuck to our game plan and didn't give them too many opportunities.
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"Maybe it was a little bit of a pull but it happens all the time and you see a lot of them not given. But a point at Manchester City is still a good point for us and we'll look forward to the next game."
The Sale-born centre-back went on to blame tiredness for his side's failure to maintain their impressive start to the game.
"We were a little bit tired," he continued. "We had a big game Wednesday as well so we've had a busy week."
"With them being able to freshen up and bring on the sort of quality they can bring on, they kept us camped in our own half in the second half and we struggled to get out at times.
"But I don't think they created too many clear cut chances and our goalkeeper came to our aid a couple of times, but you'll take that, especially when you're defending a point."