If anybody's game is still showing a Stan Lee icon above the big circus tent in Central Park after you know you saved him there, your game is likely glitched, and you won't be able to currently reach 100% (maybe they'll patch?, but doubt it).
But there is a fix to get all trophies/achievements, it's just that your game will stay at 99.8 or 99.9; check this out for info on the work-around to it:
Lego games typically get 1-2 patches. We will hopefully hear word of one coming down the pipe soon. --- Only the strongest will survive; lead me to heaven when we die. I am a shadow on the wall; I'll be the one to save us all.
I replayed main story mission 15 in free play for a second time (without doing any of the minikits or saving Stan, since I did them the first time), and for whatever reason, that fixed it for me.
Others are also at 99.9 % because they're missing the boat vehicle that must be bought at a sea vehicle station. Which is easy to miss, seeing as how you basically never use boats in this one. The sea station only has two boats, one is automatically unlocked, the other costs 150000 studs, and is worth .1%.
I know this probably shouldn't go in this topic. But my problem may relate to it. I'm at 99.9% in the game and I need one more gold brick. This stan circus glitch happened to me, but I still got all the stan lee in peril and unlocked stan lee. But I'm missing a gold brick. Here's what I've completed.
I was stuck at 99.9 percent too with the Stan Lee glitch going on, but what i didn't realize is i forgot to buy the Mandarin's Boat at one of the boat vehicle stations (forgot they even existed). I got the 100 percent after that. --- 3DS FC 1719-3711-0721 Gamertag - Brokeslimjim v2 / PSN - Brokeslimjim