The company I currently work for messed up our bonus we were supposed to get on the 25th and gave some of us not even half of the amount we are supposed to get on the 10th. This is out third and final bonus and we know how they get us in taxes, it's a substantial amount, but because it's the same bonus money on 2 different checks can the remaining balance of out bonus money be taxed twice?

I read this several times and can't make sense out of it, sorry. Maybe someone else can. Can you state it more precisely?

I assume OUT means OUR? Whatever taxes they take out will be returned when you file income taxes IF you have a refund coming.

I think I figured it out. No, they can't tax twice on the higher amount just because they didn't give you the right amount. They should adjust the last bonus check to balance out the tax on all 3 amounts.
Tax on bonuses is a different rate from a regular paycheck.
Take your paystubs to payroll and ask to have them explained. If you work for a little company with an in house payroll person, take them to a tax person outside of the company.

The withholding on a bonus is substantially HIGHER than the taxes withheld on a normal paycheck.

However, the total amount you are eventually taxed is determined on your annual tax return.

As long as the Form W-2 properly reflects what you got, you will be fine.

but because it's the same bonus money on 2 different checks can the remaining balance of out bonus money be taxed twice?

The main thing you are missing here is that your bonus has NOT been taxed, yet. What was taken out of your bonus check was WITHHOLDING. Withholding is not what you pay in taxes. It is an amount estimated by the government, based on the amount of the check and the exemptions you claim on your W4 that you will owe when you file your return.

So, even if you are over withheld, you will get that back when you file your tax return next year. As ATE said, you should check your W2 when you get it in January to confirm that the correct withholding amounts are listed.

Agreed, taxes are withheld from your check on the amount of that check. Also, as noted, bonus have a higher amount withheld.

But taxes you pay, are decided when you file your taxes, and this is not based on what they withhold.