It's because laws and financial fraud are very different things to the Premier League's self created rules regarding participation in their competitions.
Looking at the charges we've been accused of the first one looks like it's regarding Mancini's time with us and the fact that he was employed by Al Jazira at the same time. As both clubs are owned by Sheikh Mansour the PL are probably saying that his pay for his Al Jazira work was actually a disguised payment for his work with City, therefore, when we told then Mancini was getting paid 'x' amount it was actually 'x + Al Jazira pay'. As long as the Al Jazira accounts show he was being paid by them and all the relevant tax or whatever was being paid then it is of absolutely zero interest to HMRC, the police or anyone else. It could however break the PL rules if they decide that it was a way of paying Mancini more than we declared, this then leads to the accusations of 'true and fair accounts' which in turn affects FFP figures. This is a PL issue rather than a fraud issue.
It will probably be the same with the player payments things, the PL will disagree with some of the figures there which breaks their reporting rules but as long as the money was reported correctly to the various countries involved then they don't care.
With the player salaries stuff it could be something as simple as Coka-Cola paid £1m to the image rights agency for an advert using NYCFC players to be put on the NY subway system. The image rights company said to them if you pay £1.1m we'll let you put De Bruyne's image on there too. This is all perfectly fine and legal and is one of the benefits of selling image rights as part of the CFG rather than as individual clubs, we can negotiate better deals for the clubs and the players involved. We then say that the payment to De Bruyne isn't part of his City wages as he was appearing in an advert for NYCFC rather than MCFC so it wasn't in the Premier League financial statement. They say that's a disguised payment as he plays for MCFC even though the work was to promote NYCFC, the PL says that breaks their rules, we say it didn't. Again, as long as all the money has been declared to the various tax officials of the countries involved it's not a legal problem but it could be a Premier League problem.
These are just examples BTW, I'm just guessing at what the actual issues are but I think it will be petty stuff like this that this whole thing is about. I just wanted to show how there's a huge difference between serious legal breaches and things the Premier League may be fussy about.