System Information
Operating system: Windows 10
Graphics card: Gtx 1080ti

Blender Version
Broken: 2.8
Worked: (optional)

Short description of error
I am trying to cut a cylinder at the intersection of an object with a screw modifier. The intersect (knife) tool does not cut straight through the mesh. Instead, It cuts and merges random points.
This is what's happening. Here is a youtube video of what I am doing.

This is what I am trying to do.

Exact steps for others to reproduce the error
create cylinder >> enter edit mode >> select one side face >> duplicate it >> extrude face >> make loop cut close to top like a small rectangle >> select that face and hit 'P' to separate into new object >> select and delete the rest of the duplicated face >> object mode and select separated face >> add screw modifier >> steps: 32, render steps: 32, screw: -0.3, interations: 6 >> apply modifier >> join object and cylinder >> select cylinder >> intersect (knife)