Internal z-order: element types below staff lines, changed since v2.1
In any score, change the color of a barline to white. It should appear as a white line on top of the staff lines, but it does not because it is behind the staff lines in the z-order. This applies to tie segments too. To see it clearly, change the color of the tie segment in the example file to white.
This is not an issue in 2.1. I have not tested earlier versions of v3.
I do not know what other elements might be drawing under the staff lines when they should not be, but hopefully we can sort out the complete list of them via this issue.