look at the docs for GaussianBlur
it says: "ksize – Gaussian kernel size. ksize.width and ksize.height can differ but they both must be positive and odd."
so, imho, you confused the kernel size with the Mat's size, try something like:
Mat mat = inputFrame.gray();
org.opencv.core.Size s = new Size(3,3);
Imgproc.GaussianBlur(mat, mat, s, 2);
return mat;