This is a known issue

If you have overlapping contours in your source vfc file and the option Remove Overlaps is turned on in the export profile, FontLab must merge contours on export automatically. Sometimes it may fail to do that due to the bug. If you noticed your glyphs in the exported font got holes where contours overlap, try to export the font two times in a row using  the File > Export Font As [profile_name] command. Use the second exported file.