I sometimes make this mistake due to the fact that I keep on forgetting that gear set loadouts are a thing and just organically swap classes by clicking my weapons instead. Which would be fine if SCH didn't make me lazy since it already has the soul stone equipped. Usually I catch it before I end up in queue but there's been a few times I've had to withdraw from said queue because it took me too long to notice. Thankfully though I haven't actually loaded into an instance without a soul stone since ARR, and probably would expire from embarrassment if I did.

That said I see this happening for a few reasons:
1. They're like me and they just plain old made a mistake.
2. If they're returners who haven't played since ARR they might be under the mistaken assumption that it's still a viable strategy, since back then the cross-class system could allow someone to be at least not a complete burden without their soul stones.
3. They genuinely don't care since most people aren't going to kick them unless they seriously hamper the run.