When I use Mocha in after effects it shrinks the object I apply the export tracking data to

I don't see any Surface setup in your Mocha UI. The Splines define the texture you are tracking, and everything inside the spline should be on the same plane (flat Surface). The Surface defines what is being tracked. You have to turn on the surface tool. That is the little blue box with the S inside. Then you must align the four corners and the center with what you want to track. When you do a corner pin attachment, a comp-sized layer will be transformed to match the Surface you define. 

You will find examples and instructions in the Mocha Essentials training course. I provided a link.

If you are applying Corner Pin to the ship, you must ensure that the Surface is the size you want the ship to be in the composite, and you have to ensure that the Ship layer fills the comp panel. If you have to scale it to make it fit, you must pre-compose and move all attributes before you apply Corner Pin.

If you just want to match motion, just track Transformation and apply that data to the Ship layer. The ship's position will match the Center of the Surface in Mocha, and the scale will not change.

If you track Transformation, Scale, Rotation, and Skew, the layer will follow all of the data you tracked. 

Unfortunately, your screenshots do not show us how you tracked the sky and objects on the horizon. 

Agree with my colleagues, we need mor info. Anyway you need to know that if you are using corner pin instead of transform options on exporting trakcing data, the target layer MUST be the same size as the tracked layer to avoid an offset. Also, every time you click ob the export tracking button with the corner pin option active, you will get several Corner Pin effect instances in your target layer and this could cause what you are talking about: layers that cannot be seen.

Agree with Rick. Show us some screenshots. From footage interpretation not matching to using a camera track without actually having a matching camera in the comp I could imagine a ton of things going wrong. Impossible to know without more specific details.

Mylenium

I would have to see your workflow. I need embedded screenshots of your Moca UI when you are tracking and the comp timeline with the modified properties in the Mocha layer and the layer that is shrinking. Pressing 'uu' will reveal all modified properties. You can copy and paste the screenshots to the reply field on the forum, drag them here, or use the Toolbar so we can see them without downloading.

I suspect there is something wrong with your workflow inside Mocha.

Have you gone through the Mocha Essentials training series?