In shippuden we learned that if someone absorbs nature energy incorrectly or over do then it would turn them into a stone toad. This was shown during the Pain attack arch when one of the paths of pain attempted to absorb Naruto’s chakra while Naruto was in sage mode, this resulted in the pain turning into a stone toad. So if Nue was to absorb uzumaki Naruto’s Chakra while Naruto himself was in the sage mode, then surely Nue would turn into a stone toad. So Naruto could have stopped Nue by just letting Nue absorb his sage Chakra turning Nue into a stone toad.

In fiction, plot error is a gap or incompatibility in a storyline that goes against the flow of logic established by the naruto shippuden story.

For example, it would be a plot hole if, for whatever reason, the upper level ninja in Hidden Leaf were unaware or uninvolved in this crisis and didn’t try to resolve it, but they did, Uzumaki Naruto himself actively attempting to resolve it when Nue appeared.

In this case, Uzumaki Naruto activated his Nine-Tails Chakra Mode, not sage mode, in order to attack Nue, and was warned not to because it might absorb his chakra and grow bigger and explode. This is sound logic.

and Even assuming naruto thought of using the Sage mode to attack, let’s look at the logistics of that.

Sage mode has to hold still to create sage chakra. In regards to Pain, he had Uzumaki Naruto in a headlock and absorbed his chakra. Naruto used this to his advantage to feed the sage chakra that caused it to become a stone toad.

Nue aborbed chakra by eating and attacking people and was the size of several buses stacked on top of each other. Needless to say, only the hold still and let it over eat is not a sound method of combating that and attacking it clearly in sage mode Chakra would not guarantee either being able to do enough damage or feed it enough sage chakra to make stone toad.

The long and short of it is, Uzumaki Naruto’s vast power and ability was actually a detriment to him in this case as it also made him a huge liability if Nue managed to absorb his chakra.