The way to deal with players who fall into a pattern is to throw them curves that disrupt the pattern and force them to adapt. The hard part about this is doing it in such a way that it doesn't just look like you the GM are picking on them. (You are, in a sense, but you're also trying to keep the game from being completely pointless.)
It's quite likely that the PCs have made a few enemies over the course of their adventures...maybe even ones they aren't aware of, like the upper-level bosses of some people they thwarted. These enemies fall roughly into two groups:
Weaker enemies. Have them compare notes and find a reason to work together against their common foe (the PCs). This can be especially effective if the groups have complementary skills, especially if they can lead the PCs into thinking only one of their old enemies is after them, then hit from an unexpected direction.
Stronger enemies. These guys have resources of their own, and are often far less scrupulous about how they use them. Maybe they find out who the PC's favorite equipment suppliers are, then buy them out (Sorry guys, I don't have that today!) or substitute faulty goods (which fail at a critical juncture). Or they get the name of their go-to hacker buddy, and kidnap a relative (or the buddy!). Perhaps they try to pin some kind of crime on the PCs, who then have to be very careful who they talk to in order to avoid getting nabbed by law enforcement. Maybe they own that building, and have made a few changes that aren't in the official blueprints. Or maybe they hired a hacker of their own, and found a way to freeze the PC's assets so that they can't just throw money at the problem. Perhaps they used some leverage on someone in the sewer department to get some work done that will totally screw up the utility of that old easy escape route.
The basic idea is to take something the PCs count on, and make it a vulnerability instead. This can be especially powerful if you're able to build the story carefully, and eventually make it clear that this isn't just some random thing...it's personal. Somebody wants payback for something the PCs did to them, and they're going to get it. Preferably slowly and painfully. Done properly (and with a group that appreciates a good challenge, rather than just the Butt-Kicking of the Week), you can turn the PCs' collective world upside-down for a while...and have the players thanking you for it. Just figure out motivations, and plan out tactics and counter-tactics based on those established PC patterns.
One thing to remember while you're at this is to avoid making everything mechanics-dependent in resolution. It's role-playing, not parcheesi; include plenty of elements that require more than just a skill roll for success. Drop clues that need actual putting together; make them talk to actual people to get information rather than just looking it up. And foreshadow some things so that later on, the players can look back and see that those innocent little bits of info you were dropping were part of a bigger (and uglier) picture.
It's a lot of work, but it is oh so worth it.