Hi Nikola!
I think I know where the problem lies. Some of the rectangles didn't get projected completely on the surface. Therefore generating extra control points (the ones you highlighted) and therefore messing up your linework.
Make sure your curves for lofting are flat and projected on the XY plane (0,0) Or to make sure move them like 1 cm down under the 0,0 XYplane. This to ensure all the rectangles fall onto the surface when projected, See attached image.
I hope this works for you, let me know!
Cheers!
Arie