Minecraft – How to make mobs follow each other in a trail

If that's actually the command you're using, there needs to be a space between the set and @e.

I'm not sure what your intending with the c argument. It shouldn't matter for the most part, but it seems useless and will only cause potential problems.

Make sure that the conditions are actually matched. Are the entities within 3 blocks? Is their "Death" score 0 (and not Null, which it starts as if not set to anything)?

The error message you are getting will happen even if the command is working as expected. After it sets the death score of nearby entities to 1, the command will fail because @e[score_Death=0,r=3,c=100] no longer targets anything. So make sure that it's this command that's actually the issue and not something else in your mechanism; this command could be working fine.

Your water elevator is misconfigured. It looks like it is flowing from under the sign, INTO your room. That is going to cause the bunching you are witnessing. I assume you are not seeing any zombies go up your water elevator.

Here's a 3 step process to make sure things are working well:

1. Make sure mobs are going up your elevator (or following whatever exit route you have designed.)
2. Make sure you have not reached the "local" mob cap. That is, the number of mobs in a 9x9x9 region around the spawner is < 6.
3. Make sure your global mob cap is not getting reached. The Spawn article on the Wiki explains this. Basically it's "Video Rendering Radius"^2 * 70 / 289. So, by default on single player this is around 70 hostile mobs.

One way to ensure 2 is to dig the floor down deeper than you have, cover it in water, and the mobs will immediately fall out of the way.