I guess you are resizing the mask with an interpolation method other than NEAREST, which would interpolate the output values and would thus create new “target” values.
So yes, I think this might be a problem assuming you are working on a multi-class segmentation use case and you should make sure that a nearest neighbors interpolation method is used.
PS: I would recommend to have a bit more patience, as I wouldn’t expect many users to be active on a Sunday and bumping after 3h of creating the topic might not have the desired effect.