Finally managed to get a screenshot of a passive ability in my skill tray.
Just before posting this I completed a fleet action and went to Earth Spacedock and noticed I had an icon on my skill tray that wasn't there before I did the fleet action. This is exactly what I was talking about earlier with the skill tray acting wonky. Passive abilities can't be placed on a skill tray, at least not manually, and it happens to me at random times. The passive ability I had on my skill tray I obtained a few days ago so it doesn't happen right after gaining a new accolade which grants a new passive ability, though it seems this was the most recent passive I earned.
I had the same after I did drag the Frequency Remodulator ability on one of my toons to a slot closer to my firing button (C1 or C2, I think). As the FR sits in one of the item slots, there was a free space there and I set all the Hypos, Nanites and Tribbles to one lower slot. After getting the Integral Frequency Remodulator from the set, I simply had to drag and drop all the abilities from the character window to the UI task bar again, in the proper order.
Thanks for your reply. I've tried again to mess with it but I can't just seem to get it to work, I don't know what to do anymore.
This problem happend after S7 when I decided to change the order of my devices in the Character menu. Once I did that the green line that appears in the UI around the devices was gone and the problem started where I have to keep dragging everything from the Availabe skills to the Tray.
All the characters I've created post S7 have this problem too.