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Although the 'Anchor Crystals' were harmless by themselves, in reality, a lot of players in the previous timeline had ended up suffering miserably before everyone realized the 'proper' way to use them.
Since the Crystals only needed to be out of the inventory to function, it might seem extremely convenient to just drop them at the last explored point before logging out, and then continue from there the next day, but that would only be possible if no one 'misplaced' them in the owner's absence.
Contrary to what most believed at the moment, the world of Arcadia didn't actually 'pause' while the players weren't allowed to log in, which meant that their 'Anchor Crystals' would actually be 'abandoned' for quite a while as they progressed through the dungeon.