The first clue is Numair's Player's mask. His facade is silly enough, but brittle, and Thom is used to looking for hidden tricks.
The second is the way Numair hides himself inside Thom's own brokenness, though, Thom admits, Numair does not entirely realize what he is doing. Thom has known the mage just long enough to know the man is not consciously cruel.
The third is actually Numair's vanity. If that vanity were an intrinsic part of Numair, he wouldn't throw himself at the wonders of nature in quite the way he does.
The grass stains and mud splatter are far more natural to Numair than the peacock finery.
The fourth is the carefully circumspect way Numair talks of anything before Tortall - before Legann, in truth. Sure, he mentions Tyra and Carthak, but Numair has a liar's sense of when the truth is actually necessary.
The fact that he smiles when talking of Carthak just screams the lie.
The fifth is the way Numair cooks. As much as Thom enjoys the mage's cooking - and Thom is actually honest with himself on occasion - it owes far more to camp food, to quick things cooked fast in one pot on the run, than Numair is aware of.
That Numair credits his cooking to dim memories of a Tyran childhood - that could probably stand as a clue on its own.
Thom stirs the soup gingerly, and wonders idly what would happen if he offered Numair cooking lessons.
The sixth is the way Numair flirts with every buxom blonde he stumbles across, though admittedly, it takes Thom a while to realize this.
The seventh is the way Numair starts flirting with him.
The eighth clue comes on a ship to Carthak, when Numair goes all quiet and stormy and fidgety and prickly in a way that is more suited to Thom himself than the normally affable mage.
What happens in Carthak is less of a clue, and more the story of Numair's torment, writ large.
Thom kills a man, deliberately, for the first and last time in his life, and as he cleans his cane with a neurotic absence, he wonders if the changes Numair has wrought in him are also a clue.
Strong hands - stronger than the mage whose they are realizes - grip Thom's shoulders and slam him into a wall. The other man is shouting something at him, Thom thinks with a dim sort of giddiness, but even now, even when Thom himself would admit it might be warranted, Numair does not force him to meet his eyes.
This is the ninth clue.