No they cannot refuse to send him his last paycheck.
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).
Usual practice in most companies. It protects them from exactly these sorts of things.
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.
Can an agreement signed when you start working really erase debt from agreement made after you started working? Seems like the second one would take precedence there.
There's also the question of labor laws. I bet this is considered wages under the law and probably impossible to sign away.
So, basically, the company can dictate the exact debts in its exit agreement? And if you disagree, you forego all claims anyway?
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.
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).