When you clean it, use a soft rag rather than a brush. I soak my BBs but there is still sometimes crud that won't come loose. I push a rag into the neck and swirl it with some cleanser. If that doesn't work, I cover a bottle brush with an old sock and use that. This cleans it up well with no scratching.
I have on bottle that didn't get this treatment and has some small scratches on the inside, but good sanitation and good cleaning allows that one to stay in the rotation.