Ctrl+pick blocking a command block and placing it down and then activating it will not actually run the command block.
Steps:
1. Make a command in a command block. E.g. /kill @e[type=slime] on a superflat world.
2. Run it by placing a redstone block next to it (it'll work)
3. Pick block it and place it again
4. Run the new command block by placing a redstone block next to it (it wont work)
5. Try again (it will now work)
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I can reproduce this using a redstone block. When using a button or a lever I did not encounter this issue