Ran the marathon in 2016 and hated the course... I'd have a hard time imagining a worse last 10k in a marathon with all those out-and-backs and loops through random neighborhoods and parks. The end of a marathon is draining enough without the added feeling that you're not making any forward progress. Thanks to Strava, I saw some people also missed turns that year, though not as egregiously as this year.
The middle miles of the course are excusable because downtown Charleston, while very nice, is not very big; there are going to be some crappy sections unless you run over some area bridges and now you're looking at a marathon with hills in an area which is famously flat.
I decided to run the half this year to avoid the terrible marathon course and it was a much better decision. The course still suffered from those crappy barren middle miles but you get all the good parts of the course without any annoying add-ons to get the distance. But it turns out a group of half marathoners ALSO missed a turn. Apparently a handful of HMers who crossed the line in the 1:20-1:30 range didn't turn towards Riverfront Park which cut about 0.7mi off the course. You can see a lot of people in the 6th-40th place range (but not all) in the results who supposedly ran their second half ~30s/mi faster than their first, which isn't evidence on its own but I've come across a couple Strava entries already that show the missed turn. Now I think I remember that turn being less obvious than the others but I still had no problem with it so this one is more on the runners than the race management, but still.
I get that this happens sometimes, but we're probably looking at ~50 affected runners between the M and HM in a not-so-huge event... that's a LOT and is pretty inexcusable. Now that said, it sounds like the race was refunding entries to those who weren't properly directed, which honestly is about as good as you're ever going to get (I also think I read that they might have been giving out free entries to Myrtle Beach marathon which is even better). Yeah they can't give you the BQ or the PR you were going to get but a lot of races would say "sorry but TS" and that would be that. Don't get me wrong, it sucks and I'd be PISSED but I think they're doing as much as they can do for right now. But as another poster(s) mentioned, the real fix is a new course... they're definitely getting a lot of feedback this year so let's see what they do with it.
Also FWIW just to be clear, there was no 3:00 pace group, there was a group of runners that were running 3:00 pace. The fastest pace group was 3:15.