Internal Server Error 500 on Multisite Subdirecoties

I did a fresh install of Multisite WordPress with Subdirectories option.

mydomain.com – Works fine
mydomain.com/wp-admin – Works fine
mydomain.com/site1 – opens but with missing styles (as if there was no style.css)
mydomain.com/site1/wp-admin – Gives Internal Server Error 500

No plugins installed – so no question of plugins conflict
No new themes installed

Any help from you all experts out there??