Operating system: Linux-5.0.7-200.fc29.x86_64-x86_64-with-fedora-29-Twenty_Nine 64 Bits
Graphics card: GeForce GTX 980/PCIe/SSE2 NVIDIA Corporation 4.5.0 NVIDIA 418.56
Broken: version: 2.80 (sub 58), branch: blender2.7, commit date: 2019-04-20 23:25, hash: rBa5d5f152dd31
Short description of error
I'm seeing two different issues:
(1) There is a broken line in the edge (see attached render). Rotating the object for a different angle, changing the boolean by moving one of the cylinders, etc. still causes broken lines, sometimes on multiple edges. Also, using the simple surface (without the toon shading setup of Shader-to-RGB and gradient) still causes the broken line.
(2) The second possible issue is that while Eeevee renders correctly otherwise, Cycles also has the broken line and in addition seems to be rendering incorrectly for the toon shade effect - i.e., all solid color vs. multiple colors expected, see attached render.
Exact steps for others to reproduce the error
Create a cube and two cylinders. Add two boolean modifiers to the cube to subtract the two cylinders. Add a toon shading setup (shader to RGB and gradient) and free style to render lines for edges. Render with Eevee and Cycles (see above). File attached.