If foo.pm defines both package Foo and Package Foo::Bar, all will be well if every program does use Foo; that is never, ever preceded by use Foo::Bar; ...

In the above case, a  use Foo::Bar; statement can never access a file  foo.pm (In Windose (sigh)) or  Foo.pm (in other, saner file systems).

... and if there is not by pure-accident a Foo/Bar.pm file anywhere in your filesystem. If there's a conflict in your package resolution ...

If there's ambiguity or conflict in file name resolution ordering, then any use or require statement can latch onto the wrong .pm file; it has nothing to do with defining multiple package namespaces within a single .pm file.

... it can be a true headache to debug.

True that, brother!