Not sure where you inferred that from - the model in the "thin walls check" preview may look a bit rugged sometimes due to the way that check decomposes and analyzes your model, but the general preview should be an accurate "what you see is what you get" image.
Any discrepancies usually arise from errors in the uploaded model - triangles with the corners listed in the wrong winding order making that part of the surface appear to be "inside out", or in your case unintended holes in the skin that make it "not watertight", i.e. not a well defined mesh object. The site software, a derivative of netfabb studio, will try to fix such problems automatically rather than reject them outright, but it has no concept of what an object "should look like", and may pick the wrong set of vertices when closing a gaping hole (across the intended opening instead of along its rim in your case).
For your original model, no "proper" price can be calculated as it is not a "proper" object - if the holes are not also apparent in your modeling software, perhaps netfabb studio basic (cross-platform freeware from netfabb.com) can help you identify and fix them.