Sometimes when I run into this, I take another look and realize that I've ignored a modifier table, or letting the characters get away with a sloppy rule interpretation. Other times, though, you've just got a grade A bunch magnificent bastards at your table.
The previous statements about using the setting are exceptional. Might I also suggest that you've missed out on some opportunities to have a point or two of background count? Magic labs/storage facilities, other mages' hideouts, or even just a mana static spell can ruin your adept's day, not to mention snuff out a support spirit or two.
Keep in mind there are plenty of ways to create tension for a character besides going for their damage boxes. Sometimes it requires a lot of this: (
http://tvtropes.org/pmwiki/pmwiki.php/Main/XanatosGambit). It sounds like you know your players and their characters well, and can plan for their responses. As their public awareness rating rises (and it sounds like these fellas make the rounds on the underground trids once in a while), they're bound to catch either the attention or the ire of someone who can do the same. This can lead to a variety of inventive setups that either play to the characters' weaknesses or rely on them leaning on their strengths and thus, also, playing into your hands.
For instance, the Johnson they beat had to work for someone, right? And
that guys's a patient sumbitch. He's waited all this time learning about who the group's major supporters are (their friendliest Johnsons/fixers, etc.). Then he arranges for the blackmailing/kidnapping/entrapment/etc. of a close personal contact, to be avoided on on the completion of mission/missions against their own backers, probably the ones with whom he has the most beef. All while planting breadcrumbs of evidence pointing to his own political/criminal/personal enemy, who's too powerful for him to touch but at whom he's happy to throw his other enemies all day long. If the team kicks the door down on his enemy, he wins (probably killing off their contact just for spite). If they attack their own backers in their usual style (probably blowing their loyalty), he wins. And if they eventually put all the pieces together and finally get to go kick that guy's ass, they'll talk about it forever. And isn't that really why we go through all that work in the first place?