As Maxby said, using a pencil to dodge negatives was a very common (almost ubiquitous in the professional field) methodology back in the day. No doubt some of our older members will have done it as a matter of course in their earlier years.
You might want to make sure they are not supposed to be there before removing them. Try printing a couple and see what you get first. If it is normal pencil then it will be mainly graphite, so may be soluble in water, but best to wait until one of the aforementioned experienced people pop up with suggestions: they have probably done it all before.
Cheers, Bob.