Yes, this may be correct, based on what you indicate about the costs of Aflac insurance being taken out.
According to the instructions for Box 1 of Form W-2 on page 16 of the IRS' General Instructions for Forms W-2 and W-3, the "cost of accident and health insurance premiums for 2%-or-more shareholder-employees paid by an S corporation" can be included in box 1.
However, the instructions for Box 3 indicate that such costs can be included in Box 3 "only if not excludable under section 3121(a)(2)(B)."
There is no instruction for the inclusion of such costs in Box 5.
So, to summarize: the costs of this type of insurance, for this type of employee, can result in Box 1 being greater than Box 3 and Box 5 on a Form W-2.
However… if this scenario doesn't seem to apply to you, it would probably be worthwhile to contact your employer.
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