When running /clear on a player, only items in the inventory and as of MC-75328 in the inventory crafting grid are cleared. Items stored in for example a crafting table are not cleared even though they are not stored anywhere else on the server and should technically be a part of the player's inventory.
This occurs for the following blocks:
crafting tables
anvils
enchanting tables
looms
grindstones
cartography tables
This is a feature request.