"The system cannot find the path specified." When running script with Shebang

When I try to run a python script with a shebang like `#!/usr/bin/env python` I get the error `The system cannot find the path specified.` When I remove the shebang the script works as normal however. Is this a problem with Atom starting in the wrong directory? I tried starting it from the command line in root but that didn't fix it.

This is also likely a problem for most scripts (I believe this occurs when running Perl scripts as well).