In 2020, he was accused of nepotism and favoritism by some social media users, who claimed that he cast his employees and friends in the web series Paatal Lok, which he also acted in and co-produced. Banerjee denied the allegations and said that he cast the actors based on their talent and suitability for the roles. He also received support from his co-actors and colleagues, who defended his casting choices.
In 2021, he was questioned by the Enforcement Directorate (ED) in Delhi for about nine hours in a money laundering case linked to an alleged coal pilferage scam in West Bengal. Banerjee alleged that he was being harassed and targeted by the Modi government for his political views and affiliation with the Trinamool Congress (TMC) party, led by his aunt and West Bengal Chief Minister Mamata Banerjee. The Bharatiya Janata Party (BJP) dismissed his allegations and said that he was trying to evade the law and play the victim card.
In 2016, he was involved in a car accident that left him seriously injured. After attending a rally, his car collided with another vehicle on the return journey, resulting in it overturning. He was admitted to a hospital and underwent surgery. He later recovered from his injuries and resumed his work.