Change the vertex color selector to black (I believe default is neutral gray) and use the “Set VertCol” button in the edit buttons.
As far as that being a bug, I’ve never seen it happen. I think we’ve all seen plenty of Blender wierdness but I think that’s just a part of any 3D package. Background processes such as antivirus can corrupt your files if they start running while you are saving, etc… It took me several days to discover the cause of intermittent Blender crashes I experienced with the vertex snapping tool.