There are story line incongruities in My Fair Lady as well....if you are comparing it to George Bernard Shaw's Pygmalion on which it is based.
I think that any time you add songs to a non-musical form...you will get incongruities.
Dare I mention that Scarlett O'hara had 2 extra children in the book????
You each get a flower because Tink brought up "Gone With The Wind" in which Leslie Howard played Ashley and Kevin brought up "Pygmalion" in which Leslie Howard played Henry Higgins.
I've seen "Gone With The Wind" and I read the book. While OF COURSE the book is better, the movie is great on its own merits. I confess to not having read Pygmalion. I watched the movie once a long time ago.
The difference between "Wicked" and these examples is that your examples are of things that are based on other things. They didn't attempt to work in stuff that they didn't address. There is no Will in GWTW. I liked Will a lot, but don't hold his absence against the movie. They can only put in so much.
Wicked, OTOH, is very much about the characters and the story of WoO and even works them all into the story, both as prequel and as parallel story...and yet it doesn't all mesh. You don't attempt to set the man you love on fire. And while they do kinda/sorta address that, him forgiving her does not explain WHY she would wish to actually murder him and go about attempting to do so.
That's just one example. I found myself sitting in the theater thinking, "Wait, if X, then Y..." and "How could that be if..."
They set it up to be congruous with the movie and they broke their own rules.
Again, I don't hate Wicked. I liked it - both the idea of it and the play itself. There were parts of it that I enjoyed very much. I just couldn't help but be dragged out of the story when thinking about how it didn't all blend.
I think that if you're going to set something up to go with something else...you ought to do it. It bugged me.
Doesn't seem to bug anyone else IRL or on the Dis, so I will be content to be alone in my buggedness.
But I will not abide anyone who puts it in a league with "My Fair Lady." Them's fightin words.
Nobody tromps Eliza. Or Miss Julie Andrews.