If I were to entertain IT, I'd like to know when the process began. I like to think the game isn't pulling my chain when Vendetta doesn't detect an "indoctrinated" presence within us.
The story reassures us all the way up to Thessia and Chronos (or at least, Vendetta says you're "recovering him from indoctrinated forces" on Chronos... so I assume we're not indoctrinated).
Eh, I'm not an IT supporter really, but I've always pointed out that Vendetta's comment probably doesn't apply here for two reasons:
1) Indoctrination is NOT an all-or-nothing event, but rather there are gradations of it.
And
2) Like any test ever designed in the history of science or medicine, by virtue of the nature of how tests work, EVERY such diagnostic test has a sensitivity and a specificity related to it. A sensitivity, which if that which is being detected is below a given threshold it will not be detected. And a specificity, in which the test itself can discriminate between what it is detecting and other similar phenomena.
So, it is completely reasonable to think that Shepard could have started to be subtly indoctrinated by the time Vendetta makes that comment, and Vendetta simply couldn't detect it because it was below his threshold for detection.
Meanwhile, Cerberus screamed indoctrinated out the wazoo ever since Mars at the start of the game. A prothean indoctrination detector isn't necessary to see that, merely a brain and some attention to detail.