why is one installation affecting the other?!

I made a website using wordpress. On it I have installed the classifieds plugin, your dashboard and some other plugins. I used the same installation to make another website to save me some time since uses the same functions. unbeknownst to me the changes that I made to website B transferred over website A! As a result I lost an entire day's work because of this! Why does this happen??!!

It's worth noting that website A uses a completely different cPanel and database than website B yet the changes made to website B affected website A! It's as if the changes made to website B changes the database of website A because when I go to log into website A I get the wordpress login for website B!