If you are claiming a rental expense for the utilities that you pay on behalf of the tenant, then the income reported to you in box 3 of Form 1099-MISC needs to be entered as income for your rental property.
Based on the situation you described, the box 3 income is most likely being reported on your Form 1040 Schedule 1 Line 8 rather than being associated with your rental property.
Entering the Form 1099-MISC into your tax return is just a means to get the income reported in the right place. You can either leave the box 3 information blank when you enter the form into your return and then include that amount as rent not reported on Form 1099-MISC, or add the box 1 and box 3 amounts together and enter the total as rent not reported on Form 1099-MISC. For the second choice, do not enter the Form 1099-MISC at all, just report the total amount as rental income. The IRS is more concerned that all of your income be reported versus having it entered on Form 1099-MISC.
If there is ever a question regarding your income, you will still have your Form 1099-MISC showing both amounts and that they were reported in total on your return.
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