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I have a MYSQL db that is around 3GB (when queried from mysql terminal) + files for about 3-4GB, so my disk space usage should be around 6-7GB but it says 11.6GB. Is there a way to find out where is all this additional usage coming from? Thanks

Try

du -hs ~
du -hs /tmp

?

Thanks, the tmp files seem to be where issue lies:

12:37 ~ $ du -hs ~ 2.6G /home/marcopy 12:37 ~ $ du -hs /tmp 9.2G /tmp

I cant find /tmp in the PA folders area. Sorry I am useless with linux. How do I / Can I get rid of those without affecting anything important? Would they include the MySql db?

If you are not comfortable with linux command line, you could also navigate to it from the files tab (just click on the "\" near the top left- where you see \ > home > macopy)

Otherwise, in linux command line, it is cd /tmp and then say rm -rf * from within /tmp.

Your mysql db isn't stored on disk. It is on a separate db server. You can probably get rid of the /tmp stuff- obviously if you are running some random code that somehow purposely stores stuff to /tmp then that is a problem (but that would be very weird code- nothing from PythonAnywhere would do that).