Last year, after requesting an ITIN for my wife (who is not a US citizen and thus requires an SSN-esque replacement to be able to file joint taxes), we received two letters from the IRS. One had the ITIN. The other denied our request for the ITIN on the basis that "We have already issued her an ITIN." Apparently, the IRS explains, that second letter should have immediately set my accountant and I to doing forensic debugging of their protocols, because it means that something "seriously wrong" happened to our returns.
What? Glad you asked. See, the IRS had lost my return. "What?" The paper was "in the building somewhere" -- we had gotten a receipt -- but they were unaware of what desk it was at. (Their first hypothesis was "You failed to file", and they threatened penalties for that, until being confronted with a Post Office return receipt. Which is, by the by, why you should always get a receipt.)
My accountant took over yelling at them for a while to find the return, and they eventually did, and -- miracle of miracles -- they typed it into the computer. Twice. Thus generating two separate and equal returns going through non-idempotent processes, such as ITIN generation.
When those two returns met up in the reconciliation stage, they blocked each other from processing. No one at the IRS noticed this, for approximately 7 months, until my third call to their CS line got someone to actually look at the file. She hit "delete" on the duplicate. (I really hope she was simplifying that for me, because it scares me if they can actually delete anything.) Return processed almost immediately, refund check cut 48 hours later.
I almost feel sorry for them on being unprepared to unearth potential political malfeasance, because that is after all a distraction from the day to day administration of the Revenue Code, but processing returns is, as the saying goes, "their only job."