Git pull silently removing files in the index

I think there's a bug in git pull. Doing a git pull in a fresh repository without any commits removes files in the index.

Example:

  $ mkdir foo 
  $ cd foo
  $ git init
  $ touch file1 file2
  $ git add file1
  $ ls
  file1 file2
  $ git pull https://github.com/sos4nt/empty.git master
  $ ls
  file2

"file2" is still there, but "file1" was silently removed and no error message was shown.

I'm running git 1.8.3.1

Cheers, Stefan