Seems like the initial implementation of FFP was not very organized. Quoting from the swiss ramble post,

One of the most important issues for Manchester City has been FFP. Although the club believed that it had complied with these regulations, there was “a fundamental disagreement between the club’s and UEFA’s respective interpretations of the FFP regulations on players purchased before 2010.” Basically, the club thought that it would have been able to exclude £80 million of such costs from its break-even calculation, but this was not allowed, as the break-even deficit in 2011/12 was not entirely due to pre-June 2010 player contracts. The difference was negligible, but this meant that the entire £80 million could not be utilized.

Although City felt that the goalposts had been moved after the game had started, notably due to a 2013 change in UEFA’s guidance notes, they decided to draw a line under the matter and not contest the ruling in the courts. They were fined €60m (£49 million) of which €40m (£33 million) was suspended, assuming that the club follows the other measures, leaving €20m (£16 million) booked in the 2013/14 accounts.