Scraping plastic can cause micro abrasions that allow for mold and other micro organisms to thrive. These can also form from just wear and tear.
Probably the best thing to do is simply to replace the bottle or maybe the cap can be replaced.
This is one of the reasons I try to avoid plastic/acrylic in my water bottles. But if i cant avoid it I try to opt for polypropylene and then just avoid getting it hot.