The CP2000 for education is a common notice. Although it takes a not-so-gentle approach by saying you owe money, it doesn't actually mean you do. CP2000s exist for 1098-Ts because 1098-Ts have been next to worthless.
1098-Ts prove nothing when the school reports the amount in Box 2. It means you were billed x amount. Billed doesn't mean paid. Many students take a credit based on Box 2 amounts, even when they have a scholarship pay for the entire thing in the following year. The IRS sends these notices because a good amount of students take credits for tuition they haven't rightfully paid. Starting in 2017, the IRS is revamping the 1098-T to avoid this problem.
"We don't consider amounts they billed you in box 2 as proof of actual expenses paid." What you were billed isn't necessarily what you paid. So, the IRS just wants some proof that what you were billed is close to what you paid. They don't consider being billed as proof of expenses paid, because it simply isn't proof.
Send them proof of the entire amount being paid, whenever that was. If you didn't pay the 2016 semester until 2016, then that portion is likely to be denied. You can wait for their feedback, -or- proactively amend your 2015 return to remove the Spring 2016 semester. You then want to account for Spring 2016 on your 2016 return.
The IRS already has the 1098-T, and it isn't particularly helpful. Send the IRS account transcripts showing payments to your school (and billings). You can likely pull that online. Send them 2015 and 2016.
