Sorry, not a bug, please close this.
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This bug is crazy. It's existed since at least 1.8.
I'm attaching a world with just 4 command blocks that completely demos the bug. The world is totally self-explanatory (has signs).
The weird thing is that the bug goes away if any of the following is true
you don't use the fill clock
you don't have the detector rail
you don't use a UUID
Whoops, I just realized this is not a bug, it is working as intended.
When you use the fill clock, it schedules the summon-minecart to the next tick. Then after summoning, the minecart activates the detector rail, which runs the command again, a second time. Then you end up with two minecarts with the same UUID, and so of course selectors then fail.
Moving the summoning/detector away from right-next-to-the-command-block made the bug go away, and once I realized that, I realized my error.
Sorry for the bad bug.