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the most common are unsecure passwords
old or not updated scripts on web-sites
unsecure ssh access
as long as you don´t know how the server was compromized take the server offline and analyse the log-files.
if your ssh-access was compromized then only a new server setup will be secure.
I'm using fail2ban to secure my ftp and ssh. I seen the fail2ban log file, the ssh was attacked but blocked the attacker's IP but the proftpd didn't attacked (no ftp attack entry in the fil2ban log). After I saw the proftpd log files and I seen the attacker knew the ftp names and passwords. This datas stored only the i-MSCP database and the users know this data too. The IP what attacked the ssh and the IP's (more than one) what login the ftp accounts doesn't match.