sometimes get something like this when importing and exporting data, tolerance settings (say for iges) on import and export can be used to merge data points or remove short lines (0.000001mm level of size), you may have some thing like this happening when you are scaling - a line or edge was larger than this but scaled the system may try to remove but can't (can't merge points), have come across with 3d CAD systems (not often) - try scale factor very slightly different size (0.501 rather than 0.5) or try to scale in native CAD system.