So the title is very confusing, because this is a confusing bug. It's much easier to just experience it, rather than explain it.

To reproduce:
1. Go into creative mode and select one of the creative tabs other than "Survival Inventory"
2. Drop stacks of items onto the ground, and pick them up until your hotbar is full. (Make sure you're still in the creative tab that is not survival inventory)
3. Pick up a few more stacks of items after your hotbar has been filled. (Still in a non-survival inventory creative tab)
4. Click the "Survival Inventory" button.
5. Notice how only your hotbar was filled and not your main inventory.

But wait, it gets weirder.

Follow the above steps 1-3.
This time, rather than clicking on the survival inventory, hover over an item in a creative tab, and shift-click it to pick up a stack of it. This stack should be following your cursor. Click on the survival inventory tab with this stack, and notice the same result as before. Now, drop this stack on the ground (click it outside of the GUI). Notice how the stack doesn't get picked up into the first available slot. This is because of the weird ghost items that I believe the client thinks are in the slots.

These empty slots will stay empty, until you relog, then they'll reappear as real, usable items.