Permalinks and Other Directories

Greetings,

Recently I have noticed an issue occurring between the permalinks setup, and other directories on my website I am trying to enter.

My WordPress is working on my root:
https://example.com/

The permalinks are setup to be used “as” a direcory:
/%category%/%postname%/

I have a directory on my root:
https://example.com/dir

Whenever I try to enter it, WordPress looks at it, as a directory it has created, and does not find it. WordPress uses the .htaccess to make the permalinks look “pretty” through the index. How can I fix this?

Also, if I use the default permalink it works fine, as it does not care that I am trying to enter a directory, so the .htaccess understands that.

Thank you.