The version of GraphiCraft used for the demo was not a finished version, and was known to be buggy. Recollections of people involved includes claims that they were terrified when Warhol used the flood fill, for example, because there was a known bug in flood fill that would cause it to fill memory outside the screen bitmap. So it's quite likely that there other bugs too.
As a wild guess, one possible source of problems might be that GraphiCraft might have taken shortcuts in saving that might have e.g. assumed a certain offset into some data structure to copy the palette information from the file to that changed before release, as some of these early programs were known to basically pretty much dump memory straight to file and load it back in straight into some data structure with minimal parsing and validation.
As a wild guess, one possible source of problems might be that GraphiCraft might have taken shortcuts in saving that might have e.g. assumed a certain offset into some data structure to copy the palette information from the file to that changed before release, as some of these early programs were known to basically pretty much dump memory straight to file and load it back in straight into some data structure with minimal parsing and validation.