Handle it however you like, but consider this. Any commodity cargo that is available at a discount would be snapped up by an incumbent, unless there was a complication that might make it less palatable. So, consider any cargo that is available for the PC's to purchase to be potentially problematic. The problems can occur anywhere along the line of the transaction. From the purchase end, getting the cargo to/on the ship, transporting it to its destination, finding a buyer, delivering the cargo, to getting paid for it and getting back off-planet.
I'm sure one of the third-parties that produce such things can come up with a D66 chart for each phase of the transaction for potential complications. Roll on a chart for number of complications based on discounted price, then roll on the requisite chart, and go!
For your free trader just scraping by, they might not mind taking some additional risk that the paperwork isn't all in order, or half of the shipment of Silowakin Bog-Fruit is going to germinate and create a toxic gas mid-week, or that the local mafioso thinks they own the cargo, or that it was sold to more than one ship owner, etc.
If left to the players to handle with a series of dice rolls, most systems of trade can be made to produce a good, or great, profit . It gets worse once they've got some money and have the luxury of holding onto a few tons of high-value cargo through several jumps until a great deal can be made. If the referee isn't there to deal with the little "complexities" that come with great deals on commodities, the PC's will make fat stacks of cash. We have discovered that players can often be distracted from adventure, and plots, and time-tables by potential fat stacks of Cr, so speculative trade can't simply be an automated thing that just happens in the background, or it will quickly overcome any main story you think is going on.
I had a character cross a sector and a half with another person, with no ship. Start with Cr60,000. Pay for passage for both people and have MCr2 by just after the midway point. Had I played it straight, I would likely have had MCr10+ by the time I arrived at my destination. That wouldn't have worked for the story, so I didn't play it straight, I threw multiple deals, spent a big chunk of cash on gear for the Scout-ship I was going to pick up, etc. I played it as a solo game, using Zozer's SOLO rules, and made things interesting, stopped for a couple of weeks every so often, took some suboptimal deals occasionally, and wrote up a nice narrative for the journey. I invite you to conduct a similar exercise, take careful notes, write up a log of your travels. 😉
