I think your 3d model is non manifold: there are intersecting faces.
You should separate each meshes to individual objects in blender ( P > separate ), and combine them with boolean operations, to finally have just one manifold mesh. Don't forget to make the face normals consistent before ( ctrl + N ). Then you can export the combined object: select it, and when exporting, check the box "apply modifiers".
If done right, no need of repairing the STL.
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