This is a testament of either your poor reading ability or memory.
1. Neji couldn't tell clones apart because Naruto perfectly divided his chakra among them to camouflage himself from the crowd
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2. Neji had already fallen victim to a clone feint once because of the reason listed above: Naruto was incredibly tactful with dispersing his chakra and using false attacks and misdirection of his real self. 359 degree vision doesn't compensate for that. Naruto was 1 step ahead of Neji as Neji himself pointed out
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3. Neji turned off his Byakugan to talk shit. This is when Naruto used another feint because he "never lost faith in his abilities" as said by Genma and came in for the final strike
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Neji exhibited douche-like behavior and paid the price for letting his guard down. It actually makes more sense than most in this entire series.
He deactivated his byakugan, thinking he had the match in the bag. It made perfect sense. Very much like how Hashirama waited for Mdara to deactivate Sharingan so he could use his clone as a feint.
All those geniuses saying 'plothole', please read the manga again. And actually understand it this time.