Consider to open the STL file in a program such as meshmixer and slice it with Edit, Plane Cut to see what the internal section of the STL file shows. The layers in S3D appear to present a construction artifact, indicating that the file creator did not use union or merge to join the entities. S3D also has an error utility that may clear those artifacts. If the STL file is not proprietary, consider to post it with your message. I would like to see the insides.