Mind you, any answer given is always "In My Traveller Universe"...
Pilots and/or ship captains have to file a flight plan in order to leave ports that have any level of flight control. On worlds that do not have this, then people can visit such worlds without fear that their flight plans are not going to be recorded and sent elsewhere. On the flip side however, are these Class A and B starports, possibly even C starports that can and do record your flight plan.
So what goes into the flight plan? What forms/papers are required to be filled for such flights? Passenger and crew manifest? Check. Cargo manifest? Check. Destination? Check
So, who gets this information in the end? In My Traveller Universe (IMTU), the Office of Naval Intelligence gets it. The Ministry of Commerce also gets this information. Each ship gets a transponder with a valid transponder code wired into it. Yes, it is something that can be spoofed, but the point is - data anomalies get detected by sophisticated software and bumped up for review by people, who in turn determine whether or not the anomaly gets further investigated. Said information on ships that are in default, get assigned to Skip tracers within a sector or subsector where the ship was last reported in. Said information is also sold to skip tracers or perhaps the organization is given a portion of the "fee" for recovering a skipped ship.
Now for the real bad news:
The Imperium is involved in the regions between worlds. The Banks and other financial institutions are based on WORLDS. The laws pertaining to the skipped ship will depend upon the laws of the financial institution as based upon the contract that was drawn up when the ship was first funded and sold to the owners in question. Some worlds may be very lenient, some worlds may specify that after a ship has been delinquent in payments for more than a year, the Felons (and I largely suspect the value at which they will have committed a felony will have been met) are now wanted individuals regardless of whether they are found with the ship or not.
Can a crew be treated as felons? Probably not. Can the captain be held accountable for commanding a ship that is in arrears? I'd suggest the answer is yes. The moment a ship is declared to be in arrears, the captain's papers are placed on the "suspended list" for a year, and revoked after that time is up. Given the nature of slow communications - I would venture to guess that only extenuating circumstances (requiring a review board to rule on it) can revise a revoked license. If the captain can be determined to have aided and abetted known felons in committing a crime (and failure to turn yourself in will be a crime) - then the Captain also becomes a Felon...
In short? Just sic the law on the skipping ships and eventually, they will be caught. Refueling is done by companies who follow the world's laws. It would make only TOO much sense for ships that have liens against the, show they have a clean, up to date payment profile or their ship can't be serviced. Same with the maintenance schedule. Same with the replacement parts shipment and ordering process.
Yes, you can engage in wilderness refueling either with a gas giant, or on worlds that permit it, from oceans. IMTU - Worlds with a Hydrographic value of 4 or less totally BAN wilderness refueling from the surface of their world. Other worlds? Remember, the law rating on those worlds are there for a reason. It is the odds that a given party of Traveller characters will be hassled by law enforcement.
As GM, if I rolled that the Law Enforcement is after the player characters, I'd set the scene with "Hi, we'd like to request a full examination of your logs for the last 12 Imperial Months. No, we have no reason to suspect anything. What? You have something to hide? Well, we have 30 ships a year that pull in here, of which 26 are well known to us due to their trade routes and habits. Four of you fit the profile for multiple skipped payment ships. We're just looking more closely at your papers is all. Are you actually guilty of non-payment of your loans? Tsk tsk tsk, now we REALLY want to look more closely at your papers in light of your not very convincing denial."
Rule #1 when heightening tension for your players - NEVER directly accuse of them of a crime unless it is blatently obvious they're guilty of it.
Rule #2 - let them get away with it ONCE so as to scare the heck out of them. If they run, the chase is on. If they don't, heighten the suspense by showing the hunt is on even if they're not directly the target of the Hunt.
Rule #3 - always wait for the weakest link in the crew to mess up.
Rule #4 - always make the first initial attempt to capture them be VERY weak. This way, if they're caught, the story progresses reasonably from that point. If they escape however, add further charges of resisting arrest, and if they engage in destruction of propery, well, that's on them.
Rule #5 - always give them enough rope to hang themselves.
Now, after you've caught them and are carting them off to prison or what have you - surprise them with an unexpected rescue. Are their rescuers pirates? Are your rescuers NOI operatives trying to infiltrate the Pirates? Are you being used as a Trojan Horse so that every contact with the Underworld you make, the Navy is able to gather that intelligence for later "clean up" further down the road? The adventure is only beginning...