I find using the line tool to be a little buggy. When creating a line with it, the layer handles are always on one side of the stroke of the line. So a line that has a 1px stroke and a 100px stroke will always have the layer handles on the same side of that stroke. I suspect that’s what’s happening here.

If I instead use the pen tool to create a line manually, the layer handles will always follow the actual vector line instead of the side of the stroke. I prefer to create lines this way. It feels more accurate. The only downside is that you have to zoom in and place your anchor points in the right spot if you want it to be pixel-perfect, which is a little more tedious.

Thanks for the tip!

I re-drew the lines using the pen tool, as you suggested, and the lines fit more consistently.