TUE = therapeutic use exemption. Basically the give you an exemption if the drug is used for legitimate medical purposes, however it typically refers to TRT. Many MMA athletes were on TRT despite being in their 20s and 30s...likely because of long term steroid abuse. it was a joke, and the athletic commissions came to their senses and banned them.
Typically the athletic commissions were doing basic panel test (testing for only 20 substances, randomized) and focusing on elevated T/E levels, I don't even think they were testing for ancillary/PCT or AI drugs. I think many of the fighters were simply using water based test suspensions, and dosing carefully.
Fairly recently, they started instituting "blood passports" meaning they would track your levels over a series of tests. In the case of Jon Jones, they tested him once, and his T levels were relatively normal. Next test soon after, they were incredibly low, with unexplained T/E ratio (though withing the 6.1 limit), suggesting exogenous test. I believe that since he was managing his dosing/ levels effectively, and perhaps monitoring his own bloodwork, they moved on to more and more agressive panels focused on AIs and PCT drugs. USADA also has anonymous snitch hotlines, with pursue a known users training partners, etc. They are pretty slick.
To answer the original question, Jon Jones was almost certainly taking short acting test shots - google his name with bodybuilding and you will see how he packed on 20-30 pounds of pure muscle, overnight, when he took on powerlifting during his latest suspension. He was taking the Letro as an Aromatase Inhibitor to prevent side effects, and Clomid for PCT. A person VERY well informed on the topic told me that he believes that they just started utilizing greatly advanced tests that can detect metabolites much longer than previous methods. This would explain the sudden influx of positive tests.
I am relatively new AAS, and have actually never cycled (yet So please feel free to correct me if any of my information here is incorrect.