The short answer is: the model is not a solid, it's not watertight.
The model consists of two separate shells: a solid base and a spherical part that is just an open shell without thickness.
It seems like the walls for the holes are completely missing, the top face of the base plate is superfluous and the two parts are not properly connected to each other.
Does this help?
Sorry I didn't look at your model but there's something wrong with the model. Maybe the normals are wrong. Go into mesh fixes - make those all visible and uncheck them all - in particular it could be that "union overlapping volumes" needs to be unchecked. If this fixes your issue then this is a hint as to the problem in your model.
You can also just run your model through netfabb free repair service on the web (it's free but you have to create an account) or try meshmixer - I think it has mesh repair tools. I think there is also a mesh repair plug-in in cura you can try.
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