This is most likely an issue with the permissions on the files you are trying to work with. Being under your web root these files (for wordpress to function properly) should be owned by www-data which is also a member of the www-data group. I check to make sure this is the case connecting via ssh and running a ls -lh on the directory. You can then add your FTP user to the www-data group which should allow it to properly read/write the files there.