When you stop a repeating commandblock with /setblock later in the chain, the whole chain still runs an extra iteration. Only if the repeating commandblock itself executes the /setblock command execution is stopped immediately.

This can easily be observed with the following setup:

• Create a repeating commandblock that needs redstone
• Enter the command: /say hi
• Create a chain command next to the first (in positive x direction). It should be always active
• Enter the command: /setblock ~-2 ~ ~ stone
• Place a redstone block in negative x direction next to the repeating commandblock

What I observed is that it will print hi two times.
What I expected to happen is only one hi.

It is very interesting that if you switch the commands:

• repeating: /setblock ~-1 ~ ~ stone
• chain: /say hi
  it correctly prints only one hi.

This is a really annoying bug, because if i have loops that should terminate at some point, they always run one time to much. This messes up a lot of things like scoreboard counter, continuous teleportation.