Are some of the parts in what I assume is an Assembly interfering with each other? If they do, that can cause the Hidden-Line-Removal code to get the wrong results. There are some display options which can help mitigate this behavior.
No its just one part, I will try and put the file up later today, I want to check on my work computer to make sure its not graphics card related
What it does is covered in the Help Documentation.
I cannot say if that should be your going forward method. It depends on your parts and your company procedures / products.
Optimize Face cleans up the part, you just have to decide whether to do this on your originally imported bodies or on the end result. The latter removes parameters. I tried it on both and it improves the results in both cases. Movie attached showing Examine Geometry highlighting the Misaligned region, Optimize Face optimizing the same region, and the view updating to show the correct rendering.