I just got a 3D Printer and am still in the setup phase so I have not done a lot with it. E.g., I am waiting on a new fan for better ventilation.
The Slicers are telling me there are an enormous number of errors in my Rhino STL files that are generated from closed polysurfaces. The slicers always say there are holes. And I mean hundreds of holes.
I have not gotten far enough along to see if this causes problems downstream.
Do you want to send us the 3dm file?
Normally you could read in the STL file into Rhino and run Naked Edge display to see where the holes are.
The problem is normally that STL does not contain join information. So. if a lot of the objects share edges and faces it is not always clear where one object stops and the next object starts.
Here is some information on checking a model: Stereolithography (.stl) import/export | Rhino 3-D modeling