Hi Mala, there are some problems with the model, a couple of things I noticed were edges broken up into small fragments:



And some areas where edges are not meeting very precisely:





So yes your process here is not making optimal geometry.

re:
> Gererally - is it the wrong operation to cut a geometry with a line or cube/boolean in order to get a spline?

Well it depends on what you're going to do with it but if you're repeating these kinds of operations on splines through several iterations that's probably not so good.

I also noticed you have some "non-optimal" shall we say construction here:



It's odd that the surface has that slanted construction to it, it's better for the surface here to have a planar end and to have the slanted areas be cuts on it.

One of your other surfaces is set up like that but not this other one.

- Michael