If you've paid too much Income Tax for the year (yes, that can happen), you can choose what to do with that excess payment:
To be carried over as tax credit for next year or quarter
This means that you can declare the overpayment as a deduction from your tax due in the following year's annual income tax returns. This is the simplest, most straightforward, and recommended option.
To be refunded
This means that you will be formally going through the tax refund process of the BIR to get the refund. It's quite a lengthy and complicated process though but not impossible.
To be issued a Tax Credit Certificate (TCC)
Similar to the above, this means that you will be going through the process of getting a TCC for the overpayment. This TCC can be used for other tax related payments. The process for this is quite complicated as well but not impossible.