In a non-volatile memory programming scheme where the memory cells are programmed in two or more sequential programming passes, when there is insufficient host data to program at least some of the memory cells during the second pass, some of the memory cells may be programmed to the wrong threshold voltage. This can be prevented by modifying the programming scheme so that this does not occur. In one implementation, this is accomplished by choosing a code scheme, which does not cause the memory cells to be programmed to the wrong threshold voltage during the second programming pass, or by programming the memory cells in accordance with substitute data that would not cause the cells to be programmed to an erroneous state.