I have a team currently in a World Series. Said team includes a '70 Vida Blue, who did not throw a single pitch in the regular season.

In the playoffs, he has pitched 9 games for 13.1 innings in relief - 8 of these at 100%, the 9th at 98%, which was game 5 of the WS. Going into game 6, his fatigue level was shown at 94 (94).

The weird thing is this: after game 6, without taking part in the game, his fatigue is 87 (88). Is this a thing that is normal? I'm very confused as to how this happened, I expected maybe some recent game fatigue, but not in this way. I'm quite confident it isn't just my imagination - I was distinctly planning to have him close out game 7 at 94% if necessary.

You should send a support ticket in.  I know its weird and should not occur, but it does every once and a while.

Two likely things foolishfool:

1) Blue and the other fatigued players are partying out late night between games, and

2) seriously, it sounds like this is game appearance fatigue, not IP. If pitchers pitch several several of their team's games in a row, or too many over a short period, they suffer from appearance fatigue. This happens even if they have plenty of IP left for the season/playoffs. The other thing is to check how many innings you are having Blue and the others pitch at at time: again, even if a pitcher is not on pace to reach his season overall IP, nor pitches in too many games in a row, he may suffer from fatigue for going over his IP/G, which is listed on his real life stats. If his IP/G is 2 and you have him going 3 innings, even if he had 50 left on the year, he will be fatigued. Otherwise you could start closers and have them pitch 9 inning games with no consequences. 

See contrarian23's excellent discussion of these matters in the forum thread "Understanding Fatigue." I will try to look it up now and bump it for you.

Yeah, I'm not really surprised that he is fatigued, and he deserves to be given that link talks about underused pitchers gaining 95% usage once you hit the playoffs. I'm more surprised that his fatigue became worse after not playing that particular game. Perhaps (and this is a complete guess) fatigue is calculated in 2 different ways with one incorrectly getting priority over the other in this case. I'll put in a ticket as profcake says.

I've seen this happen before, and I confess I do not understand why it does.  I expect it is a glitch, but if there is an actual reason for it, then that is part of the fatigue formula that I don't understand.

It's a glitch.  I've sent tickets in about it, and Admin always asks for the details (which I provide), but they can never explain why it happens.  

I've also seen the opposite: a tired mopup pitcher comes in at 22%, throws 255 pitches, then the next game he's at 25%.  

One thing I've noticed is that these issues often seem to come up with pitchers who are extremely rested or tired, or who were acquired during the season (WW or trade), or who switch back and forth between starting and relieving.