The distribution amount listed on your Form 1099-R should include the income and is reported in box 1 on your Form 1099-R entry. I believe you may have reported the principal distribution in box 1 and the income portion in box 2. For instance, if you over contributed $1,000 and withdrew that plus $10 in income, the entry in box 1 would be $1,010, with $10 going in box 2. So, if your income goes up $10, you withdrew the extra $10 so you should not be over your contribution limit.
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