Each of your withholdings presumes the individual income item (wages, bonus, RSU) was your sole income. But when you add them all up, you are likely boosted into a higher tax bracket. This can also happen, for example, with married couples who both work, or folks who have more than one job. And it often catches folks by surprise at tax time, as it did you
When I was working, my spouse and I both opted on our W-4's for Single (even though married) with 0 exemptions, plus an additional dollar amount withheld. And we still owed money at tax time.