Multi-output recipes are a pain because of partial backups
Dyson Sphere Program's oil refineries are a pain because they produce two things: Hydrogen and refined oil. I need hydrogen to research technologies, but I don't need refined oil at my current level of tech. That means the refined oil tends to back up in the system. Because the oil refineries produce two things in the same recipe, if one of the things backs up then it stops executing the recipe. That means when the refined oil backs up, my refineries stop making hydrogen. Without hydrogen, my labs stop making energy cubes, which means my other labs stop researching, because at this stage every tech requires energy cubes.
(I seem to recall having similar challenges with oil in Factorio.)
When the oil backs up, I stop getting new techs. This is a pain.