No it won't help to talk to the IRS. There is nothing the IRS would/should do. The company screwed up making the deposit, however, I do not believe they screwed up the reporting. There are strict rules on when income is reported to the beneficiary and it sounds like they reported it correctly.
A couple things don't make sense. I assume you received a 1099 for 2016 and it was showing 13 payments. If true, it should also show 13 state withholdings. Your statement "..State taxes withheld from that 13th payment are gone forever" is false. If they withheld it, you can claim in on your return. If they do not show it on the 1099, have them issue a corrected 1099. The withholdings should be shown in the same year as the payment. What do you mean on your statement "I was required to have my tax for reworked with added costs"? Do you mean have them amended? Did you file your 2016 taxes before you received the 1099 for your pension? If so, that error is on you.
G23
