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I borrowed $5500 from a Roth IRA from tax year 2014 in late December of 2016 and I put the money back in within the 60 day period so that it is a rollover. I already contributed my maximum for both tax year 2016 and 2017 to this same account. I wanted to transfer the account to another institution using a trustee to trustee transfer, but there was a $25 fee so I gave the banker an extra $25 for the fee. However, I called the bank and the $25 is going to be counted as a rollover.

What are my tax consequences of this excess $25 that the bank is going to "steal" with their fees?

I am transferring the account to a brokerage firm where I will be investing the majority of the amount of the funds.

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    Your mistake was in telling the bank where you have your IRA to make a trustee-to-trustee transfer to the brokerage. If instead you had told the brokerage firm that you had an IRA with the bank and wanted to have it transferred to the brokerage via trustee-to-trustee transfer, they would (most likely) have done the whole thing for you at no cost. At least, that's the case with most mutual fund houses that offer IRAs; they waive any charges in order to get their hands on the money; brokerages might be different since your broker gets commissions on each transaction.
    – Dilip Sarwate
    Feb 9, 2017 at 14:39

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Your best bet is to remove the excess contribution. Your broker should have forms to do that. There is a 6% tax on the excess contributions for each year that it remains uncorrected. It would be better to just eat the $25 fee and get rid of any future headaches.

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