That was my immediate thought. Any decent system needs to ensure that it isn't running at a loss. To make that happen, they need an accounting system in place.
Rather than a loss, they managed a significant profit. The profit didn't go to the company.
I've seen lots of affiliate systems (sign up for a sight, the referring webmaster gets x%). In the adult industry, it's called shaving. The referring webmaster has a percentage of their sales (I've seen up to 25%), where it isn't recorded that they got the sale. Instead, it is credited to another account. The owner of the system doesn't always know. They see sales come in. They see payments go out. The shaved sales go to one of the developer's accounts (usually to a difficult to trace 3rd party).
If I were the developer, I'd have a friend in another country set up his affiliate account. The "lost" sales get paid out to him. He keeps a percentage, and pays me the rest. It can be very difficult to trace until there is a code audit. The audits don't usually come until the boss knows there's something funny going on. As long as the boss is getting a large profit, they have no reason to audit.
In the rest of the corporate world, it's skimming. Accountants can make it look like the missing funds are going to nondescript costs.
In both skimming and shaving, it becomes obvious when the person doing it gets too greedy. Like, it's difficult to justify that $1M/yr goes to miscellaneous custodian costs. And yes, I've seen exactly that, in a company that only made about $3M/yr profit. Sometimes it goes to consumable costs. It can be tricky to track if they're smart. When they get greedy, smart falls out of the equation.