I've got a repeater-commandblock, that should remove items from my inventory by the command "/clear @a[team=Player] double_plant 4 1".
When I'm in creative-mode an put a single item into my inventory, this item doesn't get removed.
Also, when it's a double_plant and I want to put it on the floor, the result of this placement is a only-top sunflower, instead of the flower, I wanted to place.
Related issues
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The cause is the same.

Not so sure it is same as MC-341. I see references to problems in 1.8 version. This bug is new in 1.9 version. I use /clear @a minecraft:lava_bucket command with a redstone clock for vanilla anti-griefing for example. This command worked fine in 1.8 but switching to 1.9 the command removes item from inventory the first or sometimes second time but usually gives error: no item in inventory to remove. This also happens when I set a command block with the command to repeating and with or without redstone input.
Are you sure that this is a duplicate of MC-341? I don't think so, because MC-341 has few to do with the "/clear"-Command or the other things that I wrote.