The problem was that he identified a poisonous plant poorly and it had the effect of preventing food digestion or absorption, so he ended up starving to death from the poison. I would imagine that this might be a hard reaction to detect at first.
How Chris McCandless Died
ODAP was identified in 1964. It brings about paralysis by over-stimulating nerve receptors, causing them to die... Considering that potentially crippling levels of ODAP are found in wild-potato seeds, and given the symptoms McCandless described and attributed to the wild-potato seeds he ate, there is ample reason to believe that McCandless contracted lathyrism from eating those seeds.
To paraphrase Homer Simpson, "The seeds are profecting themselves somehow!"