This can happen due to 1 of 2 reasons:
1 - you crawl a URL that also includes a /directory/ like this:
Site.com/products
🔥 When you enter a URL with a /directory/, by default that directory will be auto-populated in the ADVANCED SETTINGS > Include Directories
This is because 99% of the time it is the user's intention to only crawl links inside that directory.
Therefore, it will ONLY crawl pages that have the /products/ in their URL.
👉 However, If you wish to include pages outside of this directory simply select this option prior to your crawl.
2- by default we skip all URLs that have parameters ( "?..." )
example: /site.com/?some-link
Solution: Go to Advanced Settings > Turn this OFF!
We disable this because 99% of those pages are duplicate product or paginated pages that you usually don't want to crawl anyway,