Could be that Naruto wasn't using his sensory ability, you have to be trying to use it to use it. Tobirama wasn't using his here
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and we seen Karin turn off her Sensory ability so she wouldn't be sensed by Shi
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. Minato and Tobirama are sensors but haven't been using it in combat. As for Kaguya coming from behind them, as that space opened, it "shh" and you can see a look on Naruto's face
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. Then she came out and both him and Naruto felt her there as you can see from the "!!" and both knew she was there as they were sweating and had a face like they knew she was there
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. As for the speed, it was stated that Naruto wasn't as good controlling it as Minato by Yamato when he first used it here
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. Naruto left to enter the war before he was done training because he got suspicious that Yamato haven't returned and found out about the war via SM sensory. Naruto didn't just have top speed when trying to get passed A, he was moving at a speed and was trying to go faster so he still didn't have full control when he was doing it
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and do so when he was focused and needed to use it
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.Naruto didn't have any training in BM or in BSM so it's not hard to see that him not having control in the speed isn't hard. The last time Naruto used his speed was when he made a clone and saved Kakashi from Obito here
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and
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. Naruto's speed requires training to master while Sasuke can S/T is much easier to master since he can just use it and learn it better through use; he did the same with Amaterasu and Susanoo.