So with rotation a card that was in my ETC band was marked as Wild only. No problem, I just took ETC off of my deck. Problem is: even tho ETC isn’t in my deck anymore the game keeps flagging that deck with this “Invalid Sideboard” error and doesn’t let me queue into Standard.
To solve this I had to add ETC back on the deck and cut all of the cards in the band (and then cut ETC again) to be able to use that deck in Standard.
This is clearly a bug.
Edit 2: In fact I had to include ETC again, remove the whole band, save the deck, then run to find a game. After that I cut ETC out of the deck again to include the card I wanted and NOW it’s working normally.
Unfortunatelly for me the only way to fix this was to delete my whole deck and make it again… 
So, what I do is make the changes I want in my deck → “Copy” → “Done” → delete the deck → “New” and let it paste it.
My solution was to add ETC back to the deck, replace the invalid card, and then save the deck. At that point, I could do whatever I wished with the ETC. It seems that the ETC keeps the previously saved sideboard attached to that deck file even without being in the deck itself.
Bringing this back up to say that this keeps happening!
Everytime I try wanna build a deck with ETC I have to delete my old deck and create a new one with the exact same cards(!!) otherwise the matchmaking simply won’t work. I don’t see this topic in the Known Issues also.