My Supervisors are not helping in writing recommendations letters Maybe they are helping and I am the one who does not know how things really work and that's why I am seeking help here. 

I am about to finish my Master in Computer science (waiting for the oral exam). And this is the time to apply for as many as possible PhD programs. The problem is that many of PhD programs ask for at least two recommendation letters (sometimes three) and they do not accept general recommendation letter. Rather, they send to the referee's email and ask him/her to write. Therefore, for each of them my referees should write a separate evaluation. So far I got them to write for three applications (two got rejected already). However, I feel I am still at the beginning and there are so many programs I need to try. I am totally aware of the program suitability and I should not apply for a program that I'm not 100% sure I have good chance. 

Now the problem is that I chase my referees to write one letter and sometimes I miss deadlines because they are busy or not responding.  I found only this question is very useful here but the issue is I follow all steps there to help them to write my recommendation letters, but they mostly do not. I am one of top 5% students of theirs and I published three papers with them.

I feel like I am stuck between the hammer and the rock here. My question is what is the best tactic I can follow at this stage? Cut down the number of programs I apply for? Or talk to the supervisor about the issue. What advice do you have for me? I really appreciate your advice.
I don't know how many letters you're asking people to write for you. However, when there is a separate form that needs to be filled out for each letter, that is asking for a considerable expenditure of time for your advisors. You need to be aware of this, and plan accordingly. You can't ask people to fill out fifty forms for you at once, and then complain when they can't get it done!

So it's not really about applying to "as many PhD programs as possible." Your advisors should be working with you to select the schools and programs you are going to apply to, and you should be working with them to ensure that you are not placing too large a burden on them. This includes giving them a list that clearly states all the schools and programs to which you are applying, as well as the deadlines, as early as possible, so that they have time to plan accordingly. Then, if there's no response a few days beforehand, you need to send a polite email. 

But to keep sending out request after request for more letters in a season is a good way to annoy your letter writers. Organize and plan in advance.