I made my traditional IRA contribution for the 2013 tax year in April of 2014. I made my contribution for the 2014 tax year in April of 2015 and shortly thereafter received a notice from Principal that I had made an excess contribution. Apparently I had not "checked the box" on the 2013 form and that contribution was attributed to 2014. Is there any way that this administrative error can be corrected without the need to amend returns and withdraw causing penalties and fees? This was just an ignorant error.
The same thing happened to me with my HSA several years ago. I made contributions in January and February. I intended for these to be for the previous tax year, but the credit union didn't know that. Toward the end of the year, they told me that I had hit the maximum contribution for the year, and that's when I discovered the mistake. Of course, it was long after I had filed the tax return. I also asked for them to amend the 5498 forms, but was told that it was not going to happen.
Form 5498 is confusing. I just found this out today, as I just received my updated 2014 5498-SA for my HSA. My box 2 (Total contributions made in 2014) contains thousands of dollars more than the annual contribution limit. This is because the credit union decided to include the amount I paid in the beginning of 2014 for tax year 2013. They agree that their records show that these contributions were for 2013, but they decided to include it in the 5498-SA anyway, and insist that the form is correct.
The first thing you should do is confirm from Principal how much they think you contributed for each tax year. Don't just go by what is on the 5498 form, because it may not be reported on this form the way you think it should be. After you know that, you can decide what you want to do next.
One option is to amend all of your tax returns to match what Principal shows in their records. This would result in fewer contributions in 2013 (more tax due) and an excess contribution in 2014 (penalties due).
Another option for you, however, is to report the contributions on your tax returns the way you expected them to be counted. If you choose this, then you don't make any changes to your tax returns for 2013 or 2014. You should, however, make sure that you don't end up with excess contributions for 2015. Any contribution that you reported on your 2014 return should not also be counted for 2015, no matter what Principal says that you contributed. You should also make sure that Principal doesn't think that you have excess contributions for 2015; if they counted some of your contribution for 2015, then you might end up not being able to contribute up to the max for 2015. If you choose this route, and you get audited, you will need to explain to the auditor about the clerical error, and hope for the best. In your favor is the fact that you really haven't gone over any limits or cheated anyone out of tax money, as your tax forms would be correct if Principal has credited the contributions the way you had intended. But you are betting on the hope that you do not get audited, or if you do, that the auditor will see your side of the situation.
When I found myself in this situation with my HSA, I chose the second option. I did not end up getting audited, and from that point on, I made it a point to double-check the contributions I made to ensure that the credit union and I agree on which tax year the contributions belong to.