I have seen similar issues with parts i’ve edited. It has to do with the way the pads are written in the svg file. I am not sure exactly the why but I do know for me I had to remove the pads from their svg group and delete all the extra attributes in the xml and then resize the entire thing before regrouping and renaming the group.
Now with that said it looks like it is only the paste mask layer with the issue so if you are not getting a stencil cut I wouldn’t worry about it.