I also have several quest issues not completing.
Imprisoned Elf - Saved Amyro and spoke with him and with Saheila in the cave after that quest should be completed but quest stay open and when I left fort joy, quest says that I abandoned him to its fate.
Call To Arms - Killed all the Shriekers and reported back to Gareth after which he moved all the Seekers in abandoned camp ready to attack the ship but after I used fast travel they all disappeared from the camp and now quest says we left without Seekers help.
The Purged Dragon - I killed Radeka and purged Slane with wand after which he flew away from the Island as a dragon. Quest should be completed but it says that we abandoned Slane and that he must save himself.
The Arena of Fort Joy - After completing first fight and becoming champion, I couldn't pick another fight till the rest of my stay on the Island. Only conversation option I had when offering for another fight was "Not right now" and therefore quest says that I left without fully exploring fighting arena.
Withermoore's Soul Jarr - I had freed his soul but quest stayed active, he never showed at the forcefield in Braccus Tower for me to remove it and therefore quest says I did not help Lord Withermoore at all.
This is some serious issues with the quests. I just left Reapers eye so I hope that rest of the quest will close properly giving appropriate exp and rewards.