Universities in England and Wales paid £400,000 in compensation to students last year, following complaints.
In 2014, the Office of the Independent Adjudicator for Higher Education (OIA) ruled on 2,175 cases, with 200 students winning payouts.
Disputes over academic issues such as degree classification or marks for work formed 61% of complaints.
Universities UK said that two million students were covered by the system and the percentage of complaints was small.
The OIA, an independent body which runs the students complaint system in England and Wales, found 59% of complaints were found unjustified, 14% ineligible for OIA intervention, while 5% were withdrawn.
The OIA ruled in favour of 500 students or 23% of cases it looked into.
Cases where financial compensation was recommended included a dispute where a student missed part of an examination because of an administrative error by the university.
Another featured compensation for distress and inconvenience, caused by a lack of communication from a university dealing with a student's complaint about a course.
OIA chief executive Rob Behrens said: "Depending on the case, this may lead to the student being given a second chance to submit work or appeal against a decision, cancellation of a penalty imposed by a university, or financial compensation, which in 2014 reached almost £400,000.
"As importantly, the report shows that, overall, universities are doing a thorough job in dealing with the majority of complaints fairly."
The number of complaints dealt with by the OIA has remained pretty steady, at about 2,000 during the past three years.
Salima Mawji, from Match Solicitors, has represented students in cases against universities.
She said: "There is a very clear trend in students becoming more and more like consumers, particularly where they are paying £9,000 fees.
"They are aware that their education is critical to their future success and are therefore prepared to go out of their way to challenge injustices."
The legal firm is running free advice sessions in Birmingham Library, focusing on students' legal rights as they relate to education.
Nicola Dandridge, chief executive of Universities UK, said: "The shift in England from public funding to increased fees means that students are understandably, and rightly, demanding more from their university courses.
"Universities are responding to this and are also improving the amount of information to students about courses to ensure that their experience matches their expectations.
"It is important to remember that the total number of complaints found to be justified or partly justified  represents a small percentage of the two million students covered by the scheme in England and Wales."
The OIA report also said it had dealt with complaints from students involved in protests, who had been unhappy with the way their university had handled the situation.
And each year it received a small number of complaints from students who may be victims or alleged perpetrators in cases of sexual harassment and assault on campus.
It said: "It should be of concern to everyone working and studying in higher education that cases occur of unwanted physical contact, unwanted advances, initiation ceremonies, sexual innuendo and threats.
"We have made, and providers have implemented, recommendations about improving support and strengthening processes to help students, and also staff, involved in such cases.
"The OIA's role is not to judge the behaviour but to look at how the providers dealt with complaints or disciplinary cases."