Not sure if anyone else has seen this, but I got done with a fight where I used on of the randomly selected team-ups in a battle & when I started the next mission I only had the other 2 from the last fight & all the rest have vanished. I almost never use them so I’m 100% certain I had at least a dozen, but I don’t remember the last time I noticed having anything else in a mission so this could have happened a week ago.
Maybe you used a character who locked out your teamups.
I’m always confused when I use 5* Black Widow - I only have MBW teamups so when I use her 5* version, I don’t have any teamups equipped.
I’m not talking about just the teamups equipped, I mean when I go to manually select teamups there aren’t any there anymore. Thankfully my boosts are still there, but teamups now show 5/20 after I picked up a few.