Happens to everyone occasionally. Try changing how you launch your specials. After a 3 or 4 hit combo. Different champs behave differently to. Might let us know which champ you are using. Captain Marvel won't land her special 2 for anyone.
I was having trouble with that until I discovered I was waiting for the last 'move' to finish before pressing the special button and getting blocked. Now I'm quicker to move my thumb and usually hit with the special. Perhaps improving your finger timing would help
I know all of that but this is clearly a new bug seeing as how nobody had a problem with this until the last few days. Did it on a 4 hit combo as well when I played with Voodoo. Seen the same thing happen to seatin 2 days ago on his Goldblum run. Hopefully its fixed on Tuesday.
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Some get blocked more than others, not to mention their crazy reaction and recovery times.