This is an old question, but I don't see the kind of answer that I would have given. Since the question is still valid for others, going ahead and answering.
From my understanding, bonuses are taxed at a flat rate of 25%
Your understanding is incorrect. Bonuses are taxed like any other employment income, anywhere from 0% to 39.6% (at the time of this question; the top rate is lower now).
The paystub clearly separates the bonus from the paycheck in two categories, but I don't know why they were taxed as if it was a combined regular paycheck. Any ideas?
Because there is no difference between bonus income and wage/salary income. So it just appears as one big lump. This is typical.
Will this difference be given back in my next tax return or is it possible to return the check and modify how it's calculated if I talk to payroll?
You can't change the check in any meaningful fashion. You could conceivably modify your withholding for future checks. But the simplest way is to just wait until the end of the year. If your employer withheld more than is necessary, you will get a tax refund. If not, you may owe money. The bonus makes it more likely that you will get a refund, as the withholding tables don't handle variable pay well. Withholding will have no effect on how much tax is owed on your income. It will only change how much has already been paid.
You could calculate your overall tax liability using an estimate for future income for the rest of the year. If it shows that you are getting a refund, you can adjust your withholding for the remainder of the year to reduce that amount. Be careful though, if you don't withhold enough, the IRS will penalize you with both interest and a fine. The only disadvantage to withholding too much is that you lose the interest or investment returns from the money. It is riskier to withhold too much than too little.
If you do adjust your withholding, remember to adjust it back later. You don't want to withhold too little next year either. My recommendation though is just to take care of it with the normal tax filing. The modest benefits from having more money for a year aren't worth the risks in my opinion.