The problem is that, as pictured, the instructions specifically mention it's OK to use a pencil to fill in the ovals.
Moreover, the ballots strongly resemble forms used for the standardized tests that schoolchildren take. Takers of those tests are explicitly instructed to use a #2 pencil. People have gotten so used to using #2 pencils for such test forms, that, in the absence of explicit instructions (and an educational advertising campaign) to the contrary, most voters are likely to use a #2 pencil out of habit.
That's a really bad idea, in my opinion. Sure, someone could simply "lose" ballots, or replace them with phony ones. But that requires more effort; one has to destroy the "lost" ballots and possibly procure new, blank ones as well. Encouraging as many voters as possible to use indelible ink won't prevent all fraud, but it is a simple step that makes fraud that much harder.
I would not be surprised if such electronically-scanned ballots in other counties and states contain similarly poor instructions.