terminal cp command

If you filesystem is broken. There could be a directory entry for /bitbucket/sourcecode/ci/application/views/info.php, but the actual file contents are not there. This is a totally wild guess.

Is this by any chance a file that is on network storage? I'm making another wild guesses here.

If not network storage, then you might boot into the Recovery Partition and run Disk Utility verify (or repair) and see if it turns anything up.

When you 'ls' you are listing 2 files (Note the space after the first info.php file).

ls -l /bitbucket/sourcecode/ci/application/views/info.php info.php

-> you only see one line of output

I suspect the output is referring to the current directory e.g.

ls ./info.php

and not

ls /bitbucket/sourcecode/ci/application/views/info.php

Run the ls command as on the above line to confirm the file exists without the second file argument.

What has this to do with Apple?

What is your question?

PS. Are you really still running on OS X Lion 10.7 ?