Your best weapon would be intelligence.
You could use tachograph-equivalents that would record speed, position, resting times, etc. These are found on trucks, buses and other large vehicles to make sure drivers respect speed limits and stop to rest. Say, if you ever caught a ship with a falsified tachograph (or lack thereof), they'd be in trouble.
However, the tachograph would only serve to prove wrongdoing, not help catch the wrongdoer. So your first bet at catching them would be random controls. Also controls directed at companies known to play with the limits of legality. In other words, standard police work.
Second way, assuming there's some of traffic control in and out of planets like there are in naval/air ports, you would know which ships leave planet A and which arrive at planet B. If planets A and B exchange the relevant information, you could know if a ship travelled way over the limit, and maybe if they stopped on route for a suspicious amount of time. If it's a day's travel and it took them two, maybe you can start asking questions.
Another solution would be to monitor their navigational computers. I would assume a spaceship would require a space-GPS of some sort. So, much like intelligence agencies can track you based on your smartphone GPS, you could have your agencies track ships based on their onboard space-GPS. Tracking one precise ship should be fairly easy, though tracking all the ships to catch suspicious behaviours would require a little big more.
First, GPS-listening stations/satellites all over. Depending on the political structure of your world, cooperation between foreign agencies could be required. Then you'd need a way to compute all the data you gathered across the whole solar system.
Depending on the computing power at your disposal and your communication infrastructure, you may only have a daily list of suspicious activities as opposed to real-time tracking. It depends on how effective and up-to-date you want it to be.
These solutions aren't mutually exclusive. Obviously, this only works if your justice system can inflict dissuasive penalties on any offender.