Orders are not pulling from correct Inventory Location, why?

When setting up your inventory locations, you can only have one location for web shipping orders, one location for club shipping orders and one location for inbound (or admin) shipping orders. If for example Location 1 has "web shipping" selected and another location is edited or created (new) with "web shipping" selected then that new/edited location will be the default for web orders. This means that all new web orders will now be depleting from different location.

To troubleshoot, first review you locations in Settings > Locations to see which is set up with Web Shipping. You can also further investigate by looking at which location was depleted in previous order by running an Report > Inventory Report > Inventory Transactions to see where it depleted from.
Inventory Transaction

You can also investigate further by selecting "more actions" and looking at "edit history" of a Location to see who and when changes were made to location - Settings > Locations :
Inventory Transaction2