How come I ran through that item box without actually getting an item?

[Aphel]

I've noticed that the coffer sometimes deviates slightly away from the lane it's in. Though, I don't think there's anything wrong. I notice this occurring more frequently when the track becomes narrow. The lanes of the multiple courses are bent out of shape when the track becomes smaller. I think that's why it seems like the chest is in the same lane and it looks like you run through it, but you don't actually pick it up because you actually weren't in the same lane.

If otherwise, refer to Kerii's post.

That's correct. When you've raced enough, you'll realize that the boxes are all in lanes. At one point I was kinda deluded into thinking some existed between lanes but no there's no such thing. Take the 3rd Box in Sagolii for example. That box looks like it's on the 1st lane (counting from the left), but if you steer your choco all the way left you would miss it. It's actually on the 2nd lane. At that point perhaps all the lanes are all distorted and bunched up close to one another.

So in the end it's not about 'going straight for the box', it's about knowing which lane the box is in and thus position your choco in that lane to receive it.