I can confirm that this sort of situation has happen to me twice though, and they are very similar, and both were for the Champions League.
The first was back in 2015 where I won the away 2-1 and lost the home game on penalties after a loss of 1-2 at home. I could see how the game was setting things up during the home match so that the other team will be able to go through.The decisive goal for my team simply did not want to come, even in extra time. Everything was going in vain, even a penalty; a player who never missed a penalty since he joined my team, missed one in the match.
The second is as posted in the previous post in this thread. I dominated this team completely, both home and away, but could not go through to the next round. When I got the 1-1 draw away, I already felt something was wrong. But, still it can be said to be a decent result. But when the home match was played, I could see how the game was making things happen so that my team would be knocked out. Again, the decisive goals did not want to come; all efforts were going in vain. But, the opponent appeared to have scored way too easily.
I have not watched the matches for talisman and motrin cases, but it is likely that they experienced a similar sort of thing. There are similarities. From the match statistics, motrin's team also appeared to have dominated the game, but still his team lost 2-0 despite winning the away match 0-1, and hence was knocked-out of the competition.
So far, as I see it, there is virtually nothing a manager can do to change the outcome for those cases, especially the second case. I pushed my players to the max, so much that some had only 60% condition after the match. May be with time, with a lot of thinking, a possible logic explanation in terms of tactics or football may be found as there is still a small possibility of the opponent having gone through due to tactics, but as it is now, some of those matches seem to be fixed.