I have noticed GPA calculation "bug" in our University, what should I do?

What is the clever thing to do when one finds such regulations in own University which can be used on one's own good?!?

I'm so glad you asked. The clever thing would be to realize that the best way to raise your GPA is to do excellent work in all your courses. Aside from being the optimal strategy GPA-wise, this has the fringe benefit that it is the only strategy with inherent rewards beyond the GPA game.

Look, I don't know where you're enrolled, but your university has taken a step down a dark road by playing with weighting GPA's differently than the number of credits or course hours (which is the weighting which corresponds to the actual instructional time and, ideally, to the workload of the course). You're contemplating a further step down this dark road by trying to play games with their game. It is up to them how they compute the GPA. I disapprove of their strange weighting system, but do you know what's even worse than a globally enforced strange weighting system? A student who asks for "a specific GPA calculation for myself".

Just rise above. See if you can recapture the quaint idea that your goal is to learn the course material rather than attain a certain number at the end. Or, if you feel that the world has moved on and that number that you get at the end is too important to your future to so naively dismiss, then respond by GETTING BETTER GRADES. Merciful Minerva, we live in strange days.

I'd hold off on your conspiracy theories as to why the GPA is computed the way it is. You are entitled to a grade computed in an accurate and transparent manner, but if you go into this process assuming the university is out to get you, you're going to have a bad time.

(Note that from your terminology, I think that your university system may be different from the US ones I know, so take with a grain of salt.)

Credit for classes isn't assigned at someone's personal whim. If the university does have a policy of computing the GPA based on Z/2 credits for this class, that's a decision that must have been made by some committee and approved by some administrators, and there will be a record of it. Most likely, it would be published in the university's course catalog or official regulations, so my first suggestion would be to read through those carefully. If it's mentioned there, then you are expected to have understood and agreed to it, and that's the end of it. (If the policy was put in place after you entered the university, you may have the right to have the previous policy applied, but it doesn't sound like that is the case here.)

If you don't find it, it's reasonable to ask someone if they can show you where the policy is documented. (If you have an advisor or someone else assigned to advise you about which courses to take and your progress in the program, they may be helpful too.)

If you still don't get a good answer (probably unlikely), you could talk to more people (e.g. a department chair). Note that if you were told about it in advance, even informally, you'll probably be considered to have understood and agreed, and the best you can hope for is to get it more clearly documented for future students.

Throughout the process, I recommend keeping the tone of "I'm confused by the system and am trying to understand it better" rather than "you've cheated me out of my rightful grade". And always keep track of what you actually hope to gain and whether your efforts are worth it - if you lock yourself in an epic battle with the university just over "the principle of the thing", it's not going to have good results for your academic career, your relationship with your professors and peers, or your own sanity.

If your university uses a method to calculate GPA that is transparent, publicly documented, and reproducible; you will have to live with it (or transfer to another school). If GPA calculations are opaque and at the whim of some school official, that's cause for legal action (being patently unfair). Your first task is to find out which camp your GPA calculation falls into. It may seem to be a stupid formula, but if it's evenly and fairly applied (and anyone can accurately calculate their own GPA), what's your recourse?

As for "that is the case, but we don't know why", that is an unacceptable answer from the school. Someone should be able to officially tell you the reasoning behind it. It's possible that it dates back to a cheating scandal 200 years ago, or that they don't want to change it so that they can compare GPAs from year to year, but somewhere there must be a clear reason behind it. Go through the proper channels before raising a public stink about it, and don't be confrontational about it. There may be a perfectly good reason (in their minds, anyway), for calculating your GPA that way, but it should be publicly known.

The school does owe you an explanation for exactly how (and why) your GPA is calculated. They don't owe you a change in the calculations to match your expectations, or even to match "industry standards".