There are clear contradictions, not just in the Cult, but even in the idea of the Nerevarine itself. As an incarnation, it suggests to us that whomever the Nerevarine is was born as such. S/he would embody part of Nerevar's soul from birth. However, the Wise Woman states that you can only 'become' the Nerevarine. Already there's a contradiction between the definition of what it means to be an incarnation, and the means you have to go to become it. Now, maybe the Wise Woman means you're not the Nerevarine in the eyes of the people. Maybe it's not as literal as 'do these trials to become the Nerevarine'. It's more to prove you are, to win their hearts. Which is a fair point, except one thing.
I already pointed out that the word 'Nerevarine' has various meanings, only one of which is the literal reincarnation of Nerevar.
The dialogue choices given to you during the battle with Dagoth Ur. Even after all the trails, after uniting all the tribes, after proving yourself, you still have the choice to not be the Nerevarine. You can deny it, you can say no. Now, if denying the soul of the being you are meant to have embodied is not contradictory to what being an incarnation is then, well, I don't know. And if you've got a better, more enjoyable explanation for the contradictory nature of the Nerevarine, I'm all ears.
The question with Dagoth Ur is simple. If you choose "By the grace of gods and fate, I am Nerevar reborn" then you are saying that your character was fated to become the Nerevarine from the getgo, that destiny had been directing you all along. If you choose "I am a self-willed hero, and I make my own fate" then you are saying that fate was never involved with you becoming the Nerevarine, you weren't fated and destiny had no role, you made the choice - its not that you were destined to be Nerevar Incarnate and then turned your back on it, its that you were never destined to begin with.
In the choice with Dagoth Ur you're choosing whether you were controlled by fate, not whether or not you went against fate.