When escaping the the Kyln, Peter Quill's ship the Milano is at the Kyln.
Why is it there? Should it not still be on Xandar?
I think it's safe to assume that Peter Quill has not been given a life sentence at the Kyln, which means that one day, he will be released.
As such, they might store his vehicle at the Kyln so that when it is time for him to be released, he can just collect it and leave in much the same way that the Kyln also stored his (and other peoples) personal belongings.
The film's junior novelisation indicates that the Milano, along with Quill's other personal possessions was impounded by the authorities. Given that he's a visitor to the system, I'd assume that it's much the same as towing a criminal's car to a police impound lot rather than allowing it to block a (spaceship) parking space.
But she didn’t get to explain further, because at that very moment Peter saw one of the guards with his most prized possession—his headphones! While private property was confiscated from all of the inmates, it was supposed to be impounded, not stolen by the guards.
Peter handed his backpack to Gamora. “Take this and go to my ship, called the Milano. It’s the orange-and-blue one in the corner of the impound yard.”