From what I've read (between the lines) in this thread it appears that they haven't!
They've fined us regularly over the two seasons as and when the offences have occurred.
It's apparently just some (probably scouse) journalist/analyst who's compiled the list and brought it to the attention of the masses in a sensationalist way which appears like a £2m fine has suddenly been slapped onto our desk when in fact it's not.
It's just another "look at what City have been up to - bet nobody knew this" tabloid article from what I can make out, bit like that "look how City move the ball before a free-kick - they do it more than everybody else" nonsense.
If we had some paid shills in the media who could be arsed to dredge through two years worth of match reports in order to compile a list for other clubs I'd assume that many, many of those other clubs' fines would look relatively similar, but there's no traction in doing that as it's a non-story and wouldn't generate the clicks.
Just another way to get the masses to foam at the mouth and light their torches and get their pitchforks out.
Didn't you know we're the only ones who "cheat"? ;)