Tamil Tiger leader are shown speaking Hindi is quite absurd. Hindi is never a common language in Sri Lanka and thus there is no way they could be speaking anything except Tamil , Sinhala and English.
When Vikram Singh visits Kannan in Madurai Jail, police there are seen wearing a different Uniform with yellow caps. Tamil Nadu Police uniform is different.
Towards the end of the movie, Vikram sends a Jaffna Documents to Jaya. The title of the documents is written in Calibri font typeface. Calibri font was added to Microsoft Office in 2007 and was not present before.
When the messages between Jaffna and Madras were decoded by R&AW staffer Ghosh. He shows the results to Vikram on flat screen monitors. Such monitors came only in the early 2000s to India. So based on the period when the movie was set in the early 90s it is highly unlikely that such monitors were procured by R&AW.
When John Abraham speaks to R&AW chief RD from Tamil Nadu after talking to the LTF defector about the hit squads he calls from a PCO (public phone booth) which has magazines hanging. The magazines have the photo of south Indian actress Sneha Naidu on their cover. Sneha was not an actress till the early 2000's in any industry and based on the time when the movie is set she would have been 10 -11 years old.
In the scene where John Abraham's character meets a former R&AW agent in Thailand, the agent says that India is among the biggest markets and the fastest growing economies of the world. This would be incorrect as during the 1990-91 period the Indian economy was doing poorly which led to massive economic reforms in 1991, which were one of the conditions of the World Bank loan to India at that time.
In the beginning of the movie , Jaffna was depicted as having mountains and lush green paddy fields and such. In reality this is totally wrong. Jaffna belongs to dry zone of Sri Lanka and has no mountains lush green paddy fields, It is nothing but dry flatland with "Thal" trees. Utterly fake portrayal.