Sometimes, I will be buying items from the main shops, and then everything goes "poof" all at once, no matter how many items there were in the shop. I use Safari. Is this a bug or am going up against super restocking ninjas? If it's a bug, is there any way to fix it?

This is normal. The shops clear out periodically to restock with fresh merchandise.

the main shops clear occasionally so that new stock can be rotated in and also just generally to keep the stock from getting so massive that it would be impossible to work with. It happens to everyone, not a bug :D

Locking since this is not a bug but is supposed to happen.