I think a part of the answer is that if you have free form replication that isn't perfect, then sooner or later something is going to emerge from that goo that realises that it's just more efficient to eat the goo. Combine that self correcting cycle with hard limits imposed by nature (presumably they need to have a power source to make it work - the goo would start to die the minute it gets to a millimetre because of inaccessible sunlight. Then there is toxicity, what happens to the waste? Heat dissipation. Structural issues and other things...) and you have the recipe for a shorter sci-fi series than Firefly. (Dear Mark, today we succeeded in making self replicating nano-robots. They were exponentially multiplying within the petri dish and then they stayed in the petri dish, because apparently nano-robots are tastier than glass and metal. Doesn't matter though, we cracked open the crate of champagne anyway.)
Which is also an argument against von Neumann probes, btw. Perfect replication isn't possible, so sooner or later you are going to see a ton of weird errors accumulate to unpredictable behaviour... (perhaps a shark that goes around "eating" other probes?)
Fungi behave much more like this. The thing we don't have an example of in nature is an intelligent creature capable of making tools that can reproduce itself from a single cell. It's definitely a hard engineering problem, but it's conceivable. It's also conceivable that such an entity could seek out and remove any malfunctioning sub-entities.
We humans actually behave a lot like that, it's just that you need at least a whole human to grow another human. It's not so strange to imagine a designed, intelligent creature that can regrow itself from a small piece.
Obviously the technical issues with self-replication are difficult, but nature was able to do it with relatively crude methods. No doubt we could eventually design something significantly better. One major advantage would be mass cooperation. Evolution has no incentive for individuals to cooperate with each other, but designed nanobots can specialize and benefit from economies of scale.
A decent illustration of this concept: https://www.youtube.com/watch?v=X-8MP7g8XOE