Nothing here is happening automatically. With the comma you are telling Matlab that you want to concatenate horizontally. If you want to concatenate vertically you can either use the semicolon, or explicitly call the cat function.
Also, your inputs seem confusing. You can get closest to your stated output by transposing your two first.
sample = [12 62; 93 -8; -1, 11];
sample2 = [10 60; 90 0; 0, 10];
new = [sample'; sample2'];