I got yer back...
Quick version: It's not a plothole because it was the Entity's doing.
that iz teh lame!!!!!1!!
Edit: Deleted my obfuscatory rebuttal; figured my 1337 could hold its own.
(sigh)
Fine, here is the long and makes me have to type more explination.
The main basis of argument to the reason that the said event (Marle's dissapearance seemingly due to Queen Leene's impending death) is a plothole is because of the grandfather paradox and how it would destroy the continuity of the timeline for the game. Look at how Marle's dissapearance actually occured. First of all, she only dissapeared once Crono had confirmation that it was her. Not when he first saw her, not when she first was mistaken for Leene. And again when she returns, it is as soon as Crono returned to the room where she dissapeared. Not as soon as Yakra was killed, nor when they safely reached the castle. See a pattern here? I certainly do.
This whole event was concocted by the entity. It needed the 600 A.D. event to occur so that Crono, Marle, and Lucca would meet Frog. Becuase without Frog they most likely would not have been able to confront Magus. Not because of a lack of power, but because they wouldn't have been able to get to the castle without knowledge of the seal on the Magic Cave and how to open it. I could go farther into how deep the entity planned but it is not needed for this discussion. So anyways, the entity needed a way to get them to meet. Leene's dissapearance proved to be excellent because Frog would be there no matter what. Without the entity sending Marle to the DBT, Crono and Lucca would have never searched for the real Leene. They would have gone back through the portal and been done with the adventure. So the entity imprisoned Marle in front of Crono, and let Lucca do the rest.
Whew, I hope that explains it.