So, I was gifted several 16 and 22oz bottles by someone that went to kegging. -- Many of the bottles had some (appears to be black) spots on the bottom of the inside. I soaked the bottles for several days in free & clear dish soap and a lot of baking soda to remove the labels. I then scrubbed the heck out of them with a bottle scrubber. Some bottles cleaned up nice, and some didn't.
The guy claims they are "hard water" deposits as he didn't rinse out the bottles when he got done using them, and beer sat in the bottle for long periods of time. -- He claimed he bottled over the top of these spots with no effects (as hard water is a "mineral" and nothing to contaminate the beer - he stated).
I tried boiling water and filling the bottles almost half way up with boiling hot water, then scrubbing them again when the bottles cooled enough to handle. This worked on a few.
I wouldn't be trying so hard to salvage bottles, but these are 16 and 22 oz and aren't bottles that I come by very often.
-I don't have star san (because we all know that would be the answer to every problem!
-I have IO Star