My tip for simulation is:
Always simulate setup and not specific toolpath
For example:
Your first setup you a block stock
You have 3 toolpaths
Rough, semi finish and finish
If you simulate everthing from beggining, when the finish toolpath starts, the material already is out.
But if simulate ONLY finish, Fusion Will assume is still all the material (block) and for Fusion, the toolpath is enter agressive into stock and error appears
If you have stock calc actived auto, sometimes, Fusion didnt had calc stock already and when simulation, Fusion assume is still already stock from the beggining.
For me, i always have automatic stock disable and always simulate from setup and jump to the end when verication is finish.
If i want to check colision, i simulate that toolpath specific, disable stock and see the colision report and try to see a specific error like shaft or holder colision