Maybe a key distinction is collaboration vs. competition. The more collaboration between individual "units" (e.g. cells in a multicellular organism or organisms in an ecosystem) the more they behave like a single thing. Ant colonies are also a strong example.
To an extent, yes. I'd say the difference is government systems. A single organism, or something like the human body, has more evolved, more sophisticated government mechanisms. The body is mostly a cooperative civilisation of cells. Of course, there's still natural competition among them, in many shapes and forms. The cells are held together in a coherent, agile, resilient organism by governance systems strong enough to keep internal Darwinism from becoming civil war.
Collaboration and competition are simultaneous. Just look at humans working in an office!