This usually should not happen. I would suggest either:
Updating pip / wheel / setuptools settings and checking, maybe this is a mistake.
Rechecking that the current shbang is something common in the script. For example #!/usr/bin/env python
Here I can not reproduce the problem:
paster --no-interactive test mkdir test/scripts echo -e "#!/usr/bin/env python\nprint('test')" > test/scripts/s.py
If you unzip this wheel, s.py will have an invalid / placeholder shbang #!python , but during the actual installation it will be changed to the correct system / virtualenv path.
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