While it is true that India did play a huge role in giving Bangladesh freedom, history is not derived from one act or event alone. To understand the sentiment today it can be broadly broken down into the following two sets of reasons:
Within four years of the liberation, the army (allegedly with the support of the Pakistani ISI, Chinese and American intelligence agencies) had taken over. Mujib’s (The founding father of the country) whole family was assassinated, except his daughter, Sheikh Hasina. And the new military regime highlighted the Islamic — rather than the Bengali identity — of Bangladesh, and India was left with barely any role.
In addition, post 1975, Bangladesh became home to Jihadist elements such as the Harkat-ul-Jihad-al-Islami with a strong anti India focus rumoured to have been funded and supported by the Pakistani ISI. When Gen. Ziaur Rahman became Bangladesh’s virtual ruler following several bloody military coups in 1975, he told the United States
that India intended to invade its small neighbor to install a puppet
Fearing a direct Indian intervention, the new regime instructed Nazrul Islam, acting foreign secretary of Bangladesh, to seek U.S. support to discourage New Delhi. This set the tone, for an entire generation of new Bangladeshi citizens to be brought up with the belief that India was a hegemony who had assisted Bangladesh only to set up a friendly puppet regime.
Even, with the return of democracy in 1990, one pole of Bangladeshi politics was taken over by BNP, which defined itself in terms of opposition to India (which by now seemed to work well to win political backing from various vote banks), flirted with Islamism, and turned a blind eye to terrorism as well as attacks against minorities.
Present Reasons (which are compounded by the historic reasons):
The two primary ones would be:
Existing political/geographic disputes: The two countries share a very long and complicated geographic border. Even post the signing of the Land Boundary Agreement in 2015, the situation of the enclaves remains tensed.
Illegal immigration: Illegal immigration from Bangladesh has been part of political discourse in West Bengal, Assam and the other North Eastern Indian States. India has from time to time raised this issue with Bangladesh including having actively pursued this issue with General Ershad and later with Begum Khaleda Zia when she visited India in 1992. Since Bangladesh refuses to accept that the Bangladeshis are illegally migrating; India decided to fence the border and has adopted a push back policy (albeit not stringently), which sometimes has resulted in tensions between the countries.
In addition to these two primary issues there are multiple issues that repeatedly cause friction between the two countries including but not limited to the water sharing dispute over the Farakka Barrage and other rivers, trade and investment issues with other regional countries such as China investing to gain greater political favour, and maritime/fishing disputes.