Most "inconsistencies" I know stem from the Perl4 to 5 switch.

Concepts where kept in the language for backwards compatibility but were "discouraged" (Well kind of)

This allowed a smooth transition for old code bases, but resulted in a lot of mental overhead and Perl getting a bad press.

At least the perldocs should have been straightened with a clear philosophy, unfortunately it's often a maze. And many core modules show still the old mindset in their docs, like Exporter

And these discouraged features still needed to be maintained, which made adding new features without breaking old ones a major headache.

It's not an easy process...Perl6 tried to break with backwards compatibility, the result is known.