As to Prachi falling off the steps deliberately to stop Milsi, now he did not expect her to go to such extreme measures to stop Milsi. He would have thought that it was a genuine accident like Milsi thought because he never overheard Ayesha's conversation with Ranvir.
As to the story being messed up because of Jay's departure, that was known more that four months back. It was not like Jay was suddenly leaving.
Although as Anushka mentioned there is a possibility that they had wanted to show Neev negative and accordingly showed all those 'clues' but later changed their mind and decided to make him positive after seeing the strong reactions to Jay being shown in a negative role.
What is the real truth only OGF knows.
I am only making some guesses and trying to give them a semblance of reason to take shelter under for all the crap they showed us.