It seems your plan administrator used the Distributions Under Employee Plans Compliance Resolution System (EPCRS). To clarify, the excess contribution to the 401(k) were employee contributions? Does the amount in box 2a include the excess contribution amount? If yes, then you might want to check with your plan administrator.
"For a return of employee contributions (or designated Roth contributions) plus earnings, enter the gross distribution in box 1, the earnings attributable to the employee contributions (or designated Roth contributions) being returned in box 2a, and the employee contributions (or designated Roth contributions) being returned in box 5. Enter Code E in box 7." (Form 1099-R instructions)
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