I fixed this by ranking her up once.

I am having this issue as well on my Hunter for at least 2-3 days now. On PC. I hadn't done any of her meditation missions on any character or selected any to do until I hit 20 on my Warlock. Selected one of the missions on the Warlock, but didn't go do it. Started doing the challenges (on my Hunter) on the planets, finished 3 the first time, got the reward from it. This last Monday night (12/11), before Tuesday downtime, I finally did the two meditation missions on my Hunter that were available from Ikora. I turned in the rep tokens I got from completing them to Ikora and bumped up my rep a little bit into that first bar. After server downtime, I came back to find her [b]green[/b] icon flashing, went to her, nothing. No new missions to pick up, no rewards, just her showing the partially filled first rep bar, the fact I can earn an engram after I hit level 20 (I am 25), and that I'll be able to buy those lvl 300 faction rewards from her once I get engrams from her. Too bad there is currently no way for me to earn anything from her to do so. It feels like's she's currently stuck thinking that she has a reward/gift for me, which is tying up the ability to get new quests from her to actually earn any. And Wed night (12/13) through Thur morning I completed 3 of those challenges in the EDZ and it shows that I should have earned a reward for doing so, but it's not giving me the reward nor did it clear the completed challenges from my screen before I logged on Thursday morning. I was able to pick up missions from Ikora on my Warlock (lvl 20ish) while this was happening on my Hunter. Please fix. I feel like I've broken my Hunter somehow and really don't want to miss out on rewards I should be/might be getting. I've just completed 5 challenges and her flashing icon turned blue and it let me turn it in for 3 rep tokens. Which gave me an engram, my first from her as far as I know. Now that I've turned all of that in, she's still flashing green. And I just now completed a Meditation mission on Titan on my Warlock and after I turned in the rep tokens I got from it, her icon is blinking green on the menu where it wasn't before I finished the mission and turned it in. I can still pick up the 'Utopia' mission she offers.

Same but for the gunsmith

You have to approach her and input the Konami Code: ↑, ↑, ↓, ↓, ←, →, ←, →, B, A, start, select. She will then offer you "hot coffee". You will want to make sure you do not have any kids in the room at this point. The flashing thing will disappear and then you will be required to go to the EDZ. Once you spawn, get on your sparrow and take out 50 enemies by running them over. The last enemy will drop a key. Take the key back to Ikora. She will take you to the Vanguard door immediately opposite her, utter an incantation, and ask you to pull out your "ghost". Ghost will then insert the key, which opens the door and you step inside. I'll leave the rest for you to discover.

I have this too on my Hunter, never got exotic reward either. Got assertion aeon gives on my titan, but nothing on my Hunter when I finished the CoO story and adventures