They got Flynn for lying, Manafort on charges dating back to before he even knew Trump and a dozen or so Russians on using bots to tinker with social media; none of which will ever see the inside of a U.S. courtroom.
Mueller isn't "out there to get people", he is there to investigate all the aspects of the Russian interference and if any Americans helped them, wittingly or UNWITTINGLY....he's just trying to find out the facts...
And yes, manafort's crimes extend back years, but Mueller has the mandate to process any crimes he may come across in this Russian investigation, even if they are not related.
And he's not done with Manafort yet....he just got Gates to plead guilty and cooperate, so Manafort could have even more crimes to be charged with....
If you are investigating a robbery and in your investigation of it you find out that someone else committed murder, the investigator is NOT going to turn a blind eye to the murder.... kind of thing.... OF COURSE prosecutors investigating the robbery would bring charges against the murderer, even though that was not part of their investigation....that's just expected.....
The others that plead guilty to lying, including Flynn, committed much bigger crimes than the lying...the lying was the small charge that the prosecutors have given them, so to drop the bigger more damning crimes against them, in a plea deal for their cooperation.