If you have block that has a data value above 0 (E.g Spruce Planks) and you don't specify a data value in the command (E.g /clear @p planks), then the spruce planks won't be cleared. However, if you have oak planks in your inventory in a slot further over than the spruce, and you run the same command, it will clear the spruce planks but only the spruce planks. You have to run it again for it to clear the oak planks. I've also reproduced the issue with wool and dirt/coarse dirt.

Steps to reproduce:

1. Run /clear
2. Put spruce planks in your first inventory slot
3. Run /clear @p planks
4. The planks are not cleared from you inventory
5. Place oak planks in your secondary inventory slot
6. Run /clear @p planks
7. The spruce planks are cleared from your inventory but the oak is not