Bee didn't exactly counter it.....I mean how csn you say you countered a technique if someone has a knife pointed right at you

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Bee simply reacted an pulled his knife on Minato as well.....it didn't show exactly when Bee did it, and like you said he could have instinctively knew where he was comming from.
In the end Bee still pulled a counter in the sense that Minato was stopped from going about his business as usual. But it isn't a counter where Minato was completely off guard and opened up to be taken out