On the official forums, the Design Director has replied with the following:
"
Shadow Lords: I confirmed I am also missing guardians (I had 98% of every type/tier), now have mostly crimson & gold- the other tiers gone. We will work on this, if you are ok with leaving your guardian collection alone (don’t buy more with gems), that might be better. I will follow up with a direct message for more info.
Inputs: We are aware and looking at this with lots of video examples coming in from everyone.
Skins/Store: The Terror and Gold skins are now just unlocked for everyone, Omen colors 7-9 as well, so they are in the character select only (do not need to be in the store/collection anymore).
"