What do I do wrong?
https://imgur.com/a/PphLJh2

Could you please provide a savefile or at least steps on how you achieved this? I can't reproduce the issue on my end
I think that this is caused by the scenario, as I am unable to create the scenario well enough for it to keep the entities and still link them together. Could you please try creating a game from Freeplay? The recommended settings are to disable all resources, disable biters, disable pollution, and set map size to 64 by 64. If you didn't use the scenario, then I'm not sure what happened.
tl;dr: please submit a savefile and try creating a save from Freeplay, that fixed it for me

Factorio 1.1 Stable / newest version of the mod / no other mods
start the "Factorissimo2 Playthrough" scenario when starting a new game
select water barrel for any output

if the scenario is broken, should it be removed?

The recommended settings might be packed up into the new item in the dropdown when creating a new game, don't know how to do that but I know Space Exploration adds an item there.

Thanks for the improvement I can add, I'll try to!
The scenario has been removed in the latest version, so things should be fine now. Not sure why it was buggy, but I'll try to find that out too.