The instructions found at http://kien.github.io/ctrlp.vim assume you don't have a plugin manager. So it tells you to do the runtime path fiddling yourself (which is an incorrect assumption in this case).
If you read
When a word is added while this option is empty Vim will set it for
you: Using the first directory in 'runtimepath' that is writable. If
there is no "spell" directory yet it will be created.
You will see that vim uses the first directory that is writable in your runtime path to place the spellfile. The first directory is the ctrlp directory since you used
set rtp^= to prepend the path to the runtime path.
The first solution would just be to remove the
set rtp^=~/.vim/bundle/ctrlp.vim line from your vimrc since, that's what pathogen does for you. The second solution would be to change the spellfile with
As an FYI, a more up-to-date fork of ctrlp is found at https://github.com/ctrlpvim/ctrlp.vim