Just because you never see this issue doesn't mean it doesn't exist. It's just that the ambiguous ballots don't matter in the vast majority of elections so no one cares.
I'm not saying computers are better than paper. They each have trade-offs.
EDIT: Out of 1000 people, how many will get confused by this design? http://www.umsl.edu/~kimballd/polk.pdf
SECOND EDIT: misaligned arrows were also a problem in Florida in the 2000 election
However, that kind of efficiency isn't required at all in a ballot. Making a couple of crosses instead of lines isn't going to make a big absolute difference in terms of the entire voting process. You want to maximize other things, first and foremost making it easy to understand and easy to recognize clearly for both the voter and the people/entities who count.
There's never been any real discussion about it being complicated, confusing or needing any other kind of design change. (Which isn't to say that you couldn't make arguments in that vein.)
There's not much room for error in this design - it seems to work well for us.