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I did a little experiment on centos7, if I extract the apt module into a 'modules' folder and do puppet apply -e 'notice("foo")' --modulepath ./modules, it runs without issue. If I do puppet apply -e 'include apt' --modulepath ./modules, I get the error you are showing above.

Do you have some external thing (site.pp, External Node Classifier (like foreman or the Puppet Enterprise console) automatically applying some kind of base role? If that is the case, then you need to put the appropriate logic either in your base role to 'do the right thing', aka, not include apt if it's not a debian based system, or classify the node so it doesn't get the same base module.