You're hitting an area of her skin and disintegrating her!
Use the laser pointer built in to the weapon to aim precisely at clothes. I've so far found that boots/gloves are counted as part of the character. I think you can only remove shirt, pants, bra, and panties.
And on different characters you can remove things like braces/suspenders, masks, eye patches and fur lines. But you have to be very, very careful to aim exactly.