Don't get me started on this. Not only does it confuse the public, but it also confuses CO computers.
I took this exact flight back in Sept and because the computer sees the flight as "direct" I was sitting in the back (CLE-EWR) of the bus while seats in F went empty. I actually had even asked an agent to manually put me on the upgrade standby-list but then somehow right before boarding I disappeared off it again.
I couldn't be bothered to spend any more time griping about it to the GA though since its such a short flight anyway.
There were a few other annoyances also having to do with the computer not interpreting the 2 segments right... but I forgot the details.
What a giant PITA these flights are.