I think the confusion may be coming from the degree title. It may be that the Master by Research is a masters degree based on existing ( or ongoing ) published research, which is possible, but implies existing published research.
Research Publications mean peer-reviewed and published research work, in a set of standard journals (in IT, the ACM is the worlds primary research publisher, with a whole lot of sub journals that you an get published in)
Depending on how you have submitted your application (and I would guess that English is not your first language, so there may have been some confusion), they might be assuming that you want to use existing work for your thesis, in which case, it needs to have been peer-review published. If it hasn't, then you are not expecting to use this, so you should make this clear.
Patents are academically worthless, because there is no evidence as such that they work - they are ideas and concepts, nothing more.
I would suggest that you play down your previous work to them, use it as an indication of interest, and nothing more. The academic community has a way of doing things, and an approach that you will need to change to fit in to. It is a whole lot more rigorous than the patents application, for good reason, because the purpose is the advancement of knowledge across the discipline.