I think those 0's might have come from the previous policy, and the difference between the students may be because those other students joined the class after the fix. Could that be it?
I had that issue because I copied assignments from a previous term, and only changed the due dates after the copy. So the students were automatically "late", and got the 0, even after I changed the due dates.
To fix it, you'd need to erase the current 0s. You can do that manually, but if too many (as was in my case), I recommend downloading the gradebook into Excel, then erasing the 0s, and then reuploading.
If the class is currently active, as it seems it is, you need to worry as well about students submitting assignments between your download and upload, so choose a time where that is less likely to happen.