So with all the reporting of games not counting towards them (and me having a problem with some and not others), I double checked and noticed something that might be the issue.
I have both the LCS (C9) and LEC (MSF) passes and while both C9 games counted towards the team mission, the Misfits game did not.
The thing I noticed was that while it counted towards the team mission, the first C9 game DID NOT count towards the overall games watched mission for the week. This held true for the second day when C9's game was again the first one on for the day.
Conversely, the Misfits game was on third and finished off the overall games watched mission but DID NOT count towards the team mission.
Could the problem be that whatever code is keeping track of these viewing stats is only able to count a viewing towards one mission or the other instead of both in the instances where both conditions apply?
Just seemed worth pointing out as a potential clue to what's been bugging people.