I'm nots sure those kind of probs are covered on kara's faq, btw the main rule is simple: keep your model solid
Actually, you can try non solid models and they really often will work w/o problems, but they more likely will have problems, will be rendered in odd ways in game, will be harder to be textured, will cause TS to crash, will not be converted, will cause some poly-wasting.
The more pro/expert you are the more you will be able to create models without using strategies that can cause those problems and the more you will be able to see where those problems are and fix em.
With solid mesh I mean a mesh with all the vertices connected to the neighbor vertices.
Stupid example that should help you understanding: imagine a line with three verts, the two extremities and a vert in the middle.
(like this: x--x--x ) With solid I mean that you have three verts in a row connected by two edges. But for many reasons it can happen this: x--xx--x with the two verts in the middle not connected and sharing the same position. This is nonsolid: you have two different and separated lines that look like only one.
You will not be able to see the difference between the two situations until you try to move one of the two verts in the middle.
In your ship the connection between pods and wing is an example of nonsolid geometry (but if you are lucky it will work anyway, you just have to try)
To fix this you have to
1-pick one of the vers in the midddle and move it
2-connect manually the two verts in the middle
3- restore the first vert to it's original position
4- weld the two verts
Also triangulating should help fixing those probs.
The try to fix bad geo button is useful, but only to fix solid models with some faces screwed by TS bugs or bad operations (it's a bit long and hard to explain, I'm not sure I would be able to, and anyway is useless at this point, just use it as last resource)