That's just how erasing works, for pencils.
Erasers don't really just pick up pencil marks. They work by abrading away a thin layer of the paper, to which the pencil medium (generally graphite) has adhered. The abrasion is a sort of side effect, as the real intent is to disturb the bonds of the graphite to the paper (or cellulose) and allow the erasers to bind instead. Cheaper erasers are less binding, so work more on abrasion.
If the pencil mark is below the ink mark, then removing such a layer of paper will remove a layer with ink on it, as well. The same activity that allows the graphite to bind to the eraser also picks up the ink particles.
The ink fades, but doesn't vanish, because the nature of the ink means it penetrates further into the paper, rather than just the topmost layer.
One solution would be to apply only a basic layer of ink above the pencil, leaving you the opportunity to reapply the ink after erasure. However, if you're not dealing with completely opaque inks then layering this way may affect your end color.
Another solution is to not erase at all, and instead use a light box start out your inked worked on a completely new sheet of paper. (There are also some transferring techniques, where you could convert the pencil sketch to and underlay in ink, but I'm not versed in them enough to explain, and you could still run into opacity issues with non opaque inks).