Is this happening with a pure ArchiMate 3 (or 2 model) or with a mixed model?
If it is happening with a pure, and, therefore, semantically correct model it could be a bug.
But if it is happening with a mixed model, I suggest you upgrade everything to version 3 or downgrade everything to version 2.
The ArchiMate 3 specification indicates that changes were made to the Flow relationship.