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Brian, This is not specific to CP2 M050. We have seen this behavior for years when assembly members are locked in Workspaces. When saving an assembly members can get the status locked in the workspace and the assembly will not save. If you just need to save the assembly only (not the components) our work around is to make an empty simplified rep, Erase Not Displayed and then save the assembly.
By the way I have been testing CP2 M060 for nearly 2 weeks now and it has not crashed a single time against Windchill 10.1 M030. Running it with the latest NVIDIA 320.00 driver as recently recommended by PTC. Going into production ASAP.