Where do the responsibilities of an MS GRA doing a thesis actually end?
tl;dr Your adviser is not wrong. There are plenty of additional responsibilities and duties of maintaining a matured lab affiliation even as a MS student.

I think you went about it a wrong way. A little hill out of a molehill has been created. 

Being a GRA in a lab does not mean that the buck stops with your thesis research. I am a member in a medium sized lab based in a ECE department.  Typically, we have 4-6 graduate students, 1-2 post docs and a gaggle of undergraduate and masters students at most given times.

My Responsibilities:


Thesis research. This is primary and takes up most of my time.
Collaborative research with another graduate student. This is my secondary project and takes up a little bit of my time.
Giving talks in the lab about our works in progress.
Guest lecturing for my adviser in his courses when he is away.
Mentoring REU (Research Experience for Undergraduates) students when they come in summer.
Mentoring undergraduate and masters students from my own university in their own and lab projects.
Helping other lab members out with analysis - typically quantitative and some qualitative.
Reviewing articles written by other lab members.
Social engaging with lab members and lab visitors.
Designing presentations for lab funding reports and reviewing said reports.


I am sure I have forgotten a few more "responsibilities" but I can assure you that my work does not begin and end with just my own thesis research. It sounds like a lot but I can assure you that it really isn't and the situation is quite typical for my university and department. I have an excellent work-life balance. Now, I am a PhD student but once upon a time, I was a MS student and I had similar responsibilities.

The situation you describe is not atypical. I have seen folks in labs (which develop apps as a stepping stone to doing research) spend a lot of time actually developing the app. You are right. It takes time.  Being a member of the lab means contributing to projects which are not just your own. It is a team effort.

Your adviser has actually given you a sanity check in terms of getting a PhD admit and in terms of what other graduate students usually do. Getting a paper accepted in a prestigious IEEE transaction is quite a considerable effort and takes a long time. It seems to me that your adviser does not feel that your research will be accepted into such a venue. I also think you hit a nerve somewhere when you argued about quantum of hours and projects to be worked upon according to your GRA deal. It doesn't work like that. You are not a unionized worker. 

Research takes as long as it takes.