Apparently something happened to her eyes or sight and got the eyes of an Acolyte when she gave into the darkness.
These are some videos about eris. Some have great screen shots, even with eris pre-darkness change, as a hunter. I encourage you to each the entire video of each.
This is a short video that references the loss of her sight, but doesn't say how she got the new ones.
(5min 50sec for sight loss)
https://youtu.be/xO0eBDgnAVc
This video is great for detailing the ill-gotten mission and referenced the loss of her eyes when she gave into and became part of the darkness.
(11min 36sec turning part darkness)
https://youtu.be/xO0eBDgnAVc
This is a great video over-all, but nothing specific about her eyes.
https://youtu.be/u1DuBp4ym1w
She was stuck with crota for so long she figured screw it, I'll blow him and maybe he'll let me go. Bad idea crota skeeter all over that woken face and bam! Three eyes later and with permanent skeet running down her face crota was like I tire of you whore. Return to your realm. Now she's salty and wants him dead, but those eyes are stuck.
LORE DAMMIT READ THE LORE DESTINY HAS CREATED SOME AMAZING LORE WITH THIS DLC READ IT LIVE IT APPRECIATE THAT BUNGIE HAS TURNED IT AROUND! Really though in a couple years I think this lore could be better than halos
[spoiler]the story of oryx... Holy hell that is awesome[/spoiler]
I'm pretty sure she somehow assimilated the eyes to blend in. There's a class item that references Toland saying something about making the Hive believe you are one of them, and she also has you collect the eyes of the forsaken (pretty sure it was forsaken anyway).