Internal links look bad in google

Hi
I changed my internal links to be permalinks with content related name.
For example, I have the url https://fishingtreats.com/fishing-lures/fishing-lures/
for my post about fishing lures in a category called “fishing lures”.
When I ran the site map the links seemed to be ok, but when entering “google webmaster tools” at the “internal links” section the link to the post is called fishingtreats.com/?p=3
How can I have the same url name as the one in my site appeares at google?

Thanks for your help