I can't speak for the paperwork involved when leaving Miso, but most companies make you sign an agreement (often in the exit interview) that you are not entitled to/owed anything more than X, Y, Z items that are explicitly stated (which usually included the last paycheck and any unpaid vacation days).
Most companies that have this agreement in place also have a similar agreement when joining the company that if you forego signing the exit agreement, you forego any outstanding debts owed to you by the company.
There's also the question of labor laws. I bet this is considered wages under the law and probably impossible to sign away.
This sounds a bit illogical, but I'm not a lawyer. Another poster said it wasn't the practice at all in his years of experience, so maybe your experience does not generalize well.
You're also making an assumption that such a contract was made in this case - and it clearly wasn't, since the Miso people acknowledged their mistake here. So the guy absolutely deserves the bonus payout, even if he didn't submit the administrative form to claim it while he was still there.