No, you are not wrong.
Yes, it is shown that Sameer doesnt believe in the existence of Sikander, which again, is challenged throughout the story because the mentor and Sameer are hiding a hard disk or some information about a drug cartel (Remember he snoops around Sameer's office to search something, checks his desk and files in his absence, calls up to get some information and he is told her needs level 5 access that Rathore has, finally he poses as Rathore to retrieve a hard disk from Rathore's locker and in the end hands over some file to Arjun after which he leaves Karan and Co to go on a "mission of his life".)
It is also shown that the two have a fight in the temple on Roshni's shraad. That conversation is a mystery to me.
In a couple of their fight scenes and much after the court room fiasco, Rathore mentions how his anger has cost him and that he never listened to reason.
So although these people do not (atleast on face) concur with him, they are hiding some information that could lead him to Sikander and Arjun knows they are hiding something and they know that Arjun doubts them.
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