When James is coming out of Siddharth's kitchen he has soda bottle in his hands but the soda bottle mysteriously disappears between shots.
Anna and Sean's house catches fire but it is clearly evident that the house that caught fire was different that their house previously shown in the movie.
After the Song "Agar Tum Mil Jayo" Emraan Hashmi is buttoning up his shift and Udita Goswami receives a phone call, she has no earring. When Emraan Hashmi asks her what happened, Udita Goswami reveals that she is pregnant, she has an earring on.
After receiving phone records on fax Siddharth steals the papers, scans them and edits records to remove his phone records from the list using Microsoft word. This would be impossible as neither Microsoft word nor any other sophisticated software existed back then (around 2004-05) that could do this complicated task of editing scanned documents.
Sonia several times tries to gather evidence by obtaining phone records, insurance details and medical records by calling phone companies and going several places. In real life such investigation requires proper paper work e.g. a warrant from court.
Despite being shot on the left side of his chest from a close distance Siddharth shows no sign of discomfort or serious injury. On the other hand when Anna is shot on her back she dies immediately.
After altercation with Yadav in desperate attempt to escape Siddharth jumps off the ferry but he conveniently jumps on to another ferry where his vehicle is already in there.
Sonia's investigation is so focused on Anna that she completely ignores Sean. Any attempt to look in Sean's past should have revealed his shady and criminal past and also his connection to Yadav.
Anna's cellphone records should have revealed her phone was being actively used even after her death proving that she was still alive.