From the Chicago Methods Reporter comes this story about poorly trained election administrators and misapplied overrides. One of the affected voters writes:
“Jim and I went to vote at 7 a.m. We were given Democratic ballots and pens. But when I got to the booth, my pen didn’t work — it was like a felt-tip marker with no ink. So I went back to the desk and was told — along with several other confused voters trying to swap out their nonfunctional pens — that these were “invisible ink” pens that would not leave marks on the ballot but would absolutely be read by the scanners.
Except that they weren’t. The optical scanners were spitting out ballots until one of the election judges used a key to override the system and get the ballots into the box. After my ballot was rejected once, I got a confirmation that my vote “counted” (when the number on the ballot box blipped from 19 to 20), but Jim was given a regular ballpoint to fill in his, and it counted right away.”
The voter made enough of a fuss that they managed to get the precinct to try to “make good”. They did this by contacting the first 20 voters at that location and inviting them to re-vote.
The Chicago Tribune covers this too.
(Aside: There are voting systems that really do use special pens. For example the soon-to-be publicly described Scantegrity II system uses invisible ink on part of the ballot that is only visible when highlighted.)
All About Voting 
Even “invisible ink” pens make marks on the paper. This story is hilariously absurd, and I’m surprised the administrators are facing jail time or a fine.
The ink, however, is reactive to some marks on the paper, so it makes a differently colored mark.
In Scantegrity II, the pen makes a yellow highlighter-like mark, and a black mark when in contact with the special marks on the paper.
*are not facing…