To answer a Meta Stack Overflow question, I compiled a list of badges which have been awarded multiple times to a single user with this query. To my surprise, it includes some well-known 'one-off' badges like Autobiographer.
Here is a query which shows all 64 instances I could find on Stack Overflow. While I could imagine that this is a leftover from an account merge, in the first two instances I checked it looks more like a buggy script run. It also doesn't explain why this user is the highest Benefactor of the site.
The problem occurs for other sites like Superuser as well, though less often.