Finding intersection of two sets in MATLAB is one of the most frequently used function if you are doing lots of data merging tasks. This is achieved by intersect function. However if you would like to do the same for many sets, there are not many alternatives.
Consider that you placed your arrays into a cell vector and would like to get all intersections of a given vector among other remaining arrays and its corresponding indices uniquely. The following function will do the job for you efficiently. It is not O($N^2$) algorithm, so computational cost only grows linearly. I called this function intersectall, code is maintained in the mathworks file exchange; intersectall.