I applied for one program, but I still want to apply for other schools I applied to one Masters program in Biology which is a course-based program. Now the application is under review and will get the results at the end of next month. 
However, meanwhile , I am also looking for other schools/principal investigators to contact about my interest in their graduate programs.The reason is that I am not guaranteed an entrance to the initial school and I don't want to miss another year just because I only put all my eggs in one basket. 

Is it bad to apply for multiple schools ( by multiple I mean 3 schools total)? and how do students normally get around with requesting the reference letters from their referees for more than one application? Not all referees like writing reference letters.
It is absolutely accepted - and usually strongly suggested - that a student apply to multiple programs for grad school. Strong programs tend to be "competitive", which is a way of saying that not everyone who applies will get a spot so you aren't guaranteed to get in just because you applied. The amount suggested varies, but I've not heard anyone suggest less than 5-6, and some suggest more like a dozen (especially if some of those are departments with a very small admissions rate). So there is nothing unusual about you want to apply than more than one - you definitely should!

Reference writers usually write one letter, then make only small modifications depending on what program you apply to. I know it can feel weird to ask someone to take time for you in this way, but it's part of the job and part of what they agreed to when they agreed to write a letter for you. Be appropriately grateful, but do not hesitate to apply to a program you'd like to be able to attend for this reason. Any sensible person writing a recommendation letter wants you to get in somewhere you are excited to go, and would very much enjoy hearing a positive result for you, and are generally happy to do their part - even if it does take them a little extra time to submit letters to a few extra places.