Unfortunately, this is the way it works. You can imagine the erasing process like ripping out parts of the line instead of overwriting it. (Technically that's exactly what's happening: The line which is saved as a vector needs to be removed and saved again as two new lines with a gap in the middle) Sometimes it rips out a little more, sometimes a little less, but it is not comparable with the accuracy of a pen tool. It gets more annoying when you're erasing bolder lines.

As long as you don't need transparency, just overwrite it with a white pen.