Yes, you should remove the 1099-Q since it is not taxable. IRS Publication 970, Tax Benefits for Education states that nontaxable distributions should not be entered. You should keep the form and supporting documents with your tax file, in case the IRS does ask in a few years.
You should be able to enter it without a tax so my guess would be in the education section that the program is trying to hold some of it -up to $10,000 for the lifetime learning credit. If you don't enter the forms in a certain way, Q first, then T, you can end up with a taxable amount.
The IRS actually does say that they prefer not to deal with forms that are not taxable, I do recommend you remove it.
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