The InChI generated depends on the order of the atoms in bond definitions. The attached test cases differ only by the atom order in four bonds. In one case the bond is defined, for example, as C5-H11 in the other as H11-C5. The file input.mol produces: 1S/C3H8O2/c1-2-3(4)5/h3-5H,2H2,1H3, the file output.mol: 1S/C3H6O2/c1-2-3(4)5/h2H2,1H3,(H,4,5).
The first structure
The second structure