FA's was about payments to Sancho's agent (I think) as a way of getting round rules on signing youth players. A different matter to the UEFA one.
I think there is also one which is similar the UEFA one; the argument being that if City broke all those UEFA FFP rules, then does that mean they also broke FA rules.
It makes sense for the FA to look into the second one, although the impression I have is that it was pushed to do so by other big PL clubs. UEFA and FA have different FFP rules, but it seems unlikely that the FA one will get anywhere if the UEFA one doesn't - I'd expect it to have the same problems in proving anything.