From my perspective, the two biggest obstacles to to perfect understanding of Dharma is the apparent contradictions between "Tanha" and "Right Aspiration" and Anatta vs Buddha's condemnation of nihilism (SN 1.96: “The nihilist…goes to terrible hell…from darkness to darkness”) and his teachings on rebirth.
Tanha, "thirst" (desire) is given as the primary cause of Dukkha and yet "right Aspiration" (basically desire) is part of the 8 fold path. Clearly Buddha did not condemn "desire" if you define it as wanting something you don't have. So what distinguishes between the two?
Anatta doctrine held by some Buddhist, that there ultimately is no-soul or self and nothing really "exists" but is empty of inherent existence and therefore insubstantial and suffering is basically nihilist. This contradicts Buddha's teaching on rebirth and Nirvana (the unborn, unmade, unconditioned etc. makes liberation from the born, made, conditioned possible). No matter how you want to spin it, if your position is that the soul does not exists and there is no self outside of conditioned existence, then you are doomed to the grave and there is zero possibility for enlightenment or liberation from Samsara because how can an "illusion" that doesn't exists be "enlightened" or "saved"? The only option for a mind made illusion is to simply cease to exist once the causes that create the illusion (the body 5 kandas etc.) dies. You just fade to black, no karma, no rebirth, no Nirvana, no enlightenment no nothing. How do you resolve this seeming contradiction?