1) Poor management of department to aid students to graduate. You have to figure out all your own.
2) Most faculty does not have funding. You may have to compromise your field of interest and choose a different one instead.
3) Duration to get a PhD is 6 yrs or more . I have seen people quitting even after 5 yrs without getting a PhD
4) There is no administrative body to monitor how adviser treat his/her research graduate students and a lot of them treat badly.