Eraser tool behaves erratically, especially when working with lines. I have tried all combinations of simplify paths on or off, inverse eraser on or off, holding control or not holding control. At one moment it will erase lines just fine then, with no changes to settings, it suddenly will not erase lines but will off-set them.
I did a search on the MTC forum since there are so many more MTC users there than here and I didn’t find this reported by anyone else. I really don’t have a clue what might be happening. Have you tried rescaling the shapes much larger or much smaller to see if that changes the behavior?