I claimed Roth IRA contributions before and received a distribution this year that shouldn't be taxed. But, the account says it is not a Roth IRA. How do I fix that?

What's in Box 7 of your Form 1099-R from the account custodian?

Code 1 IRA/SEP Simple. I called E-Trade to discuss fixing that, but nothing they could do.

What you did was make nondeductible contributions to a traditional IRA, not to a Roth IRA.  If you did not previously report these nondeductible traditional IRA contributions, you'll need to amend the tax returns for the year's for which you made these contributions to report them as nondeductible traditional IRA contributions with a Form 8606 for each of those years.  Begin with the first year since each year's (usually) line 14 transfers to line 2 of the subsequent year's Form 8606.  On your 2016 tax return, your basis in nondeductible traditional IRA contributions will be applied to your 2016 distribution to minimize the amount subject to tax and penalty.

So there is no way to change these contributions to a Roth IRA, since that was always the intention but I just selected the wrong account type when it was set up?

You are too many transactions down the road to be able to do that.  Even if the contribution was made for 2016, the code 1 distribution has locked you in to it being a traditional IRA contribution.