So long as you remember to refer to things using the correct package name (HR::myFunction) rather than the file name (MyModule::myFunction), the only technical issue is that symbols exported by the package won't work automatically. If it exports anything, you'll have to manually call HR->import; after you use MyModule; because the automatic call to MyModule->import; won't do anything.

Even though it doesn't cause technical problems, it does tend to cause major usability and maintenance problems, so, as a general rule, it shouldn't be done except in very limited circumstances. A package named HR in a file named MyModule.pm is not one of those circumstances.