I would say it depends on what else you are going to include in the story as to what she might get arrested for.
First, there is always murder but that was done on the show. But you could do that and have her framed by the real killer taking blood from the scene and putting it on her clothes, leaving the murder weapon in her apartment, etc. But it would have to be someone who understands forensics to frame her even partially convincingly.
Second, with Lois breaking and enter to steal something is always a real possibility. In this instance she could have really broken in to get evidence of wrong doing by the company and an employee (somewhat high up) could have seen her so that they then stole the protype and plans for something and she is charged with industrial espionage.
Third suggestion would be assault. Lois is known to know martial arts so someone she has put in jail in the past could set her up to take an assault rap.
My fourth and final suggestion could be a real arrest. Lois didn't seem to have much respect for the police in general and could have wound up with so many parking tickets that she didn't pay that they put a boot on her car and things just escalate from there.
Just some thoughts to spark your muse.
