Check if your source mesh if composed by several not connected shells doing some test SeparateObjects.
- If this already results in several objects consider to join them to a single watertight object (ie. running EDIT/MakeSolid or joining the objects via BooleanUnion).
- If MM finds only one shell (or two in case of a hollow object) your cutting plane cuts it several times (e.g. if you do a vertical cut in a "S" shape). In this case (e.g. if you want to cut on the upper intersection of the S only) you need to run a selection based PlaneCut: Run Select and select the region where the cut is restricted to. Run Edit/PlaneCut inside SELECT.
On noisy it may happen the a global cut cuts tiny "peaks" of a tangent surface. This case run ANALYSIS/Inspector before SeparateShells and dim down the SmallThresh slider to detect only these small peaks.
If you do not want or an not combine loose pieces: Instead of doing a global separate action (EDIT/SeparateShells), there's also a selection based Separate: Navigate to a view along the cut done before and run SELECT. Click on empty space near the former cut > a red line will be drawn. generate a polygon roughly including one half but not touching the other. Now hit E to expand the selection to get one half selected totally. Now run EDIT/Separate inside SELECT.
