When you entered the information from your Form 1099-R reporting the distribution from your Roth IRA, you should have seen some messaging on the screen if you owed any additional tax on the distribution for an early distribution penalty. If you did not see that message, then you are not paying any penalty and Form 5329 is not required to claim an exception.
You also mentioned in your question that you took out your contributions from the Roth IRA to pay for qualified education expenses. As long as your distribution did not exceed the contributions that you had made to the Roth IRA, then the distribution is not taxable or penalized as an early distribution.
That is one of the benefits of having a Roth IRA. You can take out your contributions at any time without tax or penalty.
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