There's been a few major improvements on this front, coming in Alpha 12.
Now particles and fragments properly carry the material of the body they hit. So this should stop compositions appearing that weren't part of the initial mix. As well, the fragmentation, and mass transfer handling has been greatly improved, to prevent the major losses of mass that could occur previously.
We're also working hard on the rendering tech side, Georg has been doing really good work on this front, so that what you see, and what the simulation data says will match. The first part of this is coming in Alpha 12, which is aimed at improving the rendering and transition of planetoids and fragments. This is all going to be a gradual process though, as we'll add and test each piece as it's finished.
The final issue, is that in Universe Sandbox, you can create situations that don't make a lot of sense in natural contexts, or that have not been observed in the Universe so far. For instance, what's a massive solid ball of Iron the size of Jupiter look like? How does it act? Eric's been doing a lot of work on that front and trying to come up with the best answers possible to those questions.