It would help to have a blueprint of the structure as it is right now.
If you built in symmetry mode, you need to have only one set of linear c-shaped arms linked to the shipyard computer. One computer is not allowed to have two sets of C-shaped shipyard areas linked at the same time.
Building right up against the station should be fine.
When creating angles, the shipyard modules should meet face-to-face, not just edge-to-edge. In other words, when building the angle, any part of the angle should be at least two shipyard modules long, and the next part of the angle should overlap the previous part, so that there is solid shipyard modules all the way around the "C", without gaps.
Try removing the shipyard computer with symmetry off and add it back, and slave the C-shaped shipyard module sections back to the computer. (Use Shift-V to slave the entire C-shaped grouping of modules at once.)
Build a cross-member between endpoints of the C-shapes, to ensure they are all equally long.
Make sure there aren't any stray shipyard modules that were accidentally built in a strange place.
Making sure just a single array of C-shaped shipyard modules are linked to the shipyard computer should eliminate the error you described.
I almost always build with symmetry mode on, but I recommend leaving it off while you build the shipyard.
The vertical and horizontal distances of the C-shape is arbitrary, and can be almost any length, up until the game fails. The individual blocks all have to be connected to a face of the one or two adjacent modules. Every module block should only have one or two modules attached to it.
Ensure that there are no gaps in the slaved modules. Shift-V mass-slaving really helps here.
