The brain sometimes doesn’t know, and the brain sometimes is aroused but the penis isn’t. There’s not one switch that controls both – sure they are often related, but they are also reasonably often not related. You can get boners you don’t want, and you can fail to get boners you do want, most guys experience both at some stage.
As to exactly why all that is the case, and why it’s not like, say, moving your arm, I don’t know and it’d be cool if anyone knows some relevant evolutionary biology.
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