That's more of an anecdotal evidence of a shitty public university system. I don't know how it works in the Czech Republic other than from your comment, but in Slovenia, it's extremely wasteful, even though it doesn't need to be.
The primary issue is that students have awesome tax and other financial benefits. First, you don't pay tax for (I'm not completely sure, but lets say) more than the minimum wage as a student. Then, you get subsidized food (lunch coupons), free healthcare (as long as one of your parents is employed) and lots of benefits with private companies (I had a bank card that allowed me free withdrawals anywhere in the EU, even in a different currency). Personally, I don't see an issue with free healthcare (I think it should be free for everyone, as it is in the UK), but tax breaks and lunches are a unnecessary benefit.
This issue is exploited by "perpetual students" - basically, there is no incentive, nor requirement, that you finish your studies "in time". The only limit is that you can have the student status until you're 26 years old, so many people stretch their studies beyond what's necessary and work for private businesses, gaining experience and not being taxed, for several years before they complete the last exams and graduate. (Then they complain that they can't get a job, because all the businesses prefer to hire students, because they're cheaper).
If education was free, but you were required to finish on time and there were no tax benefits of being a student, the system would waste much less money. To reduce the cost even more, the government could automatically give you a "nominal loan" that was automatically canceled when you finish your study, so only people who study and don't finish would have to pay, and you'd also have to pay for any additional years you need (e.g. if you fail a year).
Watch out; independently of being an effective idea or not, this would create a strong incentive for extensive corruption.