When I clone a wiki repo through https it works as expected. When I clone the same wiki repo through ssh I get the contents of the project itself and not the wiki.

This behaviour appears to have changed at some point. I had a wiki repo that I cloned through ssh and I had successfully pushed and pulled some changes. Later trying to run hg pull results in an "abort: repository is unrelated" message.

Here's an example with random repo:
{{

{\\ $ hg clone https://bitbucket.org/ellislab/codeigniter/wiki wiki_https\\ requesting all changes\\ adding changesets\\ adding manifests\\ adding file changes\\ added 16 changesets with 15 changes to 3 files\\ updating to branch default\\ 3 files updated, 0 files merged, 0 files removed, 0 files unresolved\\ $ hg clone ssh://hg@bitbucket.org/ellislab/codeigniter/wiki wiki_ssh\\ requesting all changes\\ adding changesets\\ adding manifests\\ adding file changes\\ added 2199 changesets with 11244 changes to 483 files (+2 heads)\\ updating to branch default\\ 314 files updated, 0 files merged, 0 files removed, 0 files unresolved\\ }}

}