JediQuaker, you must have been sent from Yoda himself...
It's now fixed!
The problem was [sTORY] Assault on Tython
It wasn't a pink one, but a yellow one. When you said that, I went through my list and just started dropping every mission I had. That is when I saw the Assault on Tython. Apparently, if you have any of the story missions in your mission log, it temporarily removes it from the list or missions you can run on the various difficulties. Hence the 27/27 and not 28/28.
I've opened up support tickets for this only to be ultimately told this was a bug. I've also submitted this as a bug, and honestly feel like it still is. It should not remove it from your list entirely and prevent you from receiving weekly rewards. The description says all flashpoints selected, and they were. If it has to have 28 flashpoints selected, it should be described as such.
JediQuaker, thank you!!!!