I think you’re right, this does look like a bug. Smaller case:
1. > 1. a
>
>
> 1. c <- this should be part of the outer list
Could you put a bug report on jgm/cmark or jgm/commonmark.js?
Note: the “two blank lines breaks out of list” rule is under consideration for removal (see the “issues to resolve before 1.0” thread), so this might become irrelevant.