I want to know the reason of this issue ???

[akamit]

Recently I launched a corporate site for my company and I noticed something which I cannot fix.

I uploaded the site files to the root folder (public_html) in my cpanel perfectly I guess but today I noticed that my index.php page can be accessed with two different URLs.

Such as,
https://www.mysite.com/
https://www.mysite.com/index.php

and this is an issue of canonical url if I'm not wrong and I can see a report in google search console (Duplicate, submitted URL not selected as canonical).

I'm not sure if I've explained the issue very well. If I did then please let me know how I can remove the second URL. Google is not indexing the second URL but I still want to remove it.

[examplens]

Recently I launched a corporate site for my company and I noticed something which I cannot fix.

I uploaded the site files to the root folder (public_html) in my cpanel perfectly I guess but today I noticed that my index.php page can be accessed with two different URLs.

Such as,
https://www.mysite.com/
https://www.mysite.com/index.php

and this is an issue of canonical url if I'm not wrong and I can see a report in google search console (Duplicate, submitted URL not selected as canonical).

I'm not sure if I've explained the issue very well. If I did then please let me know how I can remove the second URL. Google is not indexing the second URL but I still want to remove it.

I am not sure where is the problem. Whatever you put in "public_html", index.php or index.html will be default page.
Usually, things like this can be solved using a .htaccess file and redirect all to www.domain.com.

[Vod]

I noticed that my index.php page can be accessed with two different URLs.

Such as,
https://www.mysite.com/
https://www.mysite.com/index.php

The index.php file is the default file for any directory. 
https://bitcointalk.org/index.php
https://bitcointalk.org

You can always change the name to something else, but Google should not index it.