Hi, I came across your site as I need to generate sitemap for my page.
My site is in https and I was testing my page which contains around 50 links to other pages within my site, also in https.

I want the crawler to crawl those pages linked to from my test page, however, the crawler is classifying the linked internal pages as "external links". I think it's because the crawler automatically attached the port number into the link and hence see that as a different domain?

For instance:
from my test page https://example.com/testpage/ the link is https://example.com/page2

your crawler would identify the linked page as https://example.com:443/page2 and classify it as External link.

I need all these page in my sitemap, is there ways around it for your software?

Default settings should automaically alias http, https and port 80 variations.

Try first turn off easy mode off
http://www.microsystools.com/products/sitemap-generator/help/easy-sitemap-generator-mode/

Then read how you can add more root domain aliases yourself:
http://www.microsystools.com/products/sitemap-generator/help/root-aliases-start-paths/
(i.e. if A1 encounters a https link and http is default, it simply "aliases" it)

If you are curious, notice that all domains in an XML sitemap has to be the exact same:
http://www.microsystools.com/products/sitemap-generator/help/multiple-domains-xml-sitemaps/