Website (with database) over a network can have a number of potential vulnerabilities.. but what the difference between 'vulnerabilities over the network' and 'vulnerabilities at the server'.. can you give me an example please..
Well, you would need to have some IDS/IPS protection to protect against network based intrusions. Vulnerabilities at the server can be caused by old software, injections done in scripts that are not secured, which can cause major problems, and so on.
This would mainly included hijacking of the network or DDoSing with Zombie computers using IRC channels. Exploiting, SQL Injections, PHP holes and unpatched software and opening in your server, backdoors etc.. can lead to your server being hacked.