What I found so far is that the issue comes from the makehtml.stripLinkDefinitions sub-parser ^1.
For the input of the example it matches C1 | C2 as a title and tries to put it back ^2. So it
combines blankLines + title, which is \n and C1 | C2, which then results in the table
being broken.
Summary
Whenever there is a footnote used above a table it will not be rendered correctly. As a workaround a comment can be placed before the actual table.
Example
Workaround