This is often because the online business is completely separate from the offline business. They have different buyers, different relationships with the suppliers, different inventories, different margins, and most importantly, different management teams running them. Why is this, you might ask?
Often what sells best offline, doesn't online, and vice-versa. A sale online could be great business online, but tank offline. So they have different sales, and feature different discounts.
In addition, some companies use the online store as a means to get rid of remaining inventory of items they're closing out. They sell them faster online. This is because shoppers expect better deals online.
Furthermore, brick-n-mortor stores carry local items that sell well in those regions, and have the authority to price them as they see fit. You usually won't find these items on their online store.
This is why you see different sales and prices online vs. offline, and why you sometimes can't find things in the store that they sell online.