No, you're not doing anything wrong. The program just doesn't like the distribution with two types of rollovers reported on the same 1099-R. The distributions should have been reported separately, one using code G for the traditional IRA rollover, and with code H for the Designated Roth Contribution rollover to a Roth IRA. But since that isn't the case, I would do exactly what you did - answer No to the question of was the money rolled over to a Roth IRA. The result is correct - a tax free direct rollover of your 401(k).
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