I just finished the Black Moon arc of the manga, and I'm a little bit confused about the part where Pluto stopped time. She did so to keep Prince Demande from making the two Silver Crystals touch, right? And, when she stopped time, everything froze, and Prince Demande didn't get to touch the crystals.

Since he didn't get to touch the crystals, I'm assuming he was frozen in time... I know that Wiseman/Nemesis was frozen. In that case, why was everyone else able to move just fine??? I don't get it...

It could be that they're the exceptions to the freeze because Pluto wills it. After all, it's one of those "I will DIE if I use it" attacks, she might as well have a moment of being omnipotent enough to do that.

I think she willingly allowed them to remain unaffected by Time Stop. Other characters started moving as shortly after time stopped while Demande and Nemesis still remained frozen.

or it could be a case of her powers don't affect other senshi? it's possible

Yeah, in the game Sailor Moon Another Story Pluto has an attack where you can freeze the opponent but no one else is frozen.

Maybe the attack (can we say it's an attack?) just affect her opponents, foes, enemies, etc. but the senshi or anyone else she is trying to protect isn't. Chibiusa was Black Lady at the time and it was stopped, if I remember well. She did something similar in anime and Uranus and Neptune weren't affected.