There are two gaps in the storyline.
1. Why did Sajid kill Subbu? Obviously, he was instructed by Sameer to do so. But, why then Sameer was also helping out Bhaskaran (Subbu's brother) in taking revenge for his brother's death? What exactly was Sameer's motive? That was never revealed.
2. What happened to Musa from Season 1? We get to see the climax of Season 1 - how people are saved from the chemical attack but what happens to the guy who set all this? Is he dead? Or is he also hiding somewhere like Sameer and Sajid? That was never revealed.