Random Pixels Being Removed From Photos?

I was going through some photos for work and noticed little black lines on the base layer that looked like guidelines. After talking to my boss we found out it wasn't guidelines and that they were randomly placed there. After going through the rest of the photos, where those black lines were the pixels were removed from the photos. I have an image example here

Anyone know how to fix  this? I've tried cloning over it and using the spot healing brush but it won't work for some reason... It's not on the photos because if I remove the base layer with the black lines theres noticable transparent lines missing from every layer.