Hi Cyrus,
Thanks for your reply!
Unfortunately the problem is yet to be fixed, I hope that my disallow will work shortly.
It seems that most of the index.php links to each other internally (and from old /index.php/ pages that no longer exist), which is super weird. How google found them does not make any sense to me.
I don't beleive that external sources are linking to these pages either - I mean, how would they find these links anyway?.