India offered no explanation of its vote. To understand India’s abstention one will have to rely on the transcript of the response by Vikas Swarup, the Official Spokesperson of the Ministry of External Affairs to a question on India’s vote:
Question: Why did we abstain at the UN Human Rights Council on the appointment of an independent watchdog for protecting LGBT rights? Does that not reflect poorly on us as a liberal democracy interested in ensuring the human rights of the LGBT community?
Official Spokesperson, Shri Vikas Swarup: As you know, the issue of LGBT rights in India is a matter being considered by the Supreme Court under a batch of curative petitions filed by various institutions and organizations. As you also know, the Supreme Court is yet to pronounce on this issue. As such we had to take this into account in terms of our vote on the third UN resolution to institutionalize the office of an independent expert to prevent discrimination against LGBT persons. 
The reasoning given for the abstention, i.e. that the matter is before the Supreme Court, does not seem to be founded on a correct appreciation of the legal position. The Supreme Court in Suresh Kumar Koushal v.Naz Foundation did uphold Section 377 of the Indian Penal Code, but in doing so had clearly stated that:
Notwithstanding this verdict, the competent legislature shall be free to consider the desirability and propriety of deleting Section 377 IPC from the statute book or amend the same as per the suggestion made by the Attorney General.
In an unprecedented decision the Supreme Court activated a little used self-corrective mechanism known as the curative remedy and ordered that the decision of the Supreme Court in Koushal to be re-heard before a five judge bench.
It should also be noted that the Supreme Court in NALSA v. Union of India, had passed another judgment upholding the rights of the transgender community to equality, dignity and expression. 
All these reasons, which indicate that the Court has made progress towards recognizing LGBT citizens as full citizens, should have emboldened the government to act. The parallel to the statements of Ghana, Botswana and Namibia in their abstention on the SOGI resolution, could not be more striking. These three countries invoked their respective Constitutional frameworks to make the case that regardless of their criminal law provision, they did not discriminate on grounds of SOGI. India instead chose to highlight the penal statute Section 377, rather than derive a policy position based on the Constitution.
While India did abstain on the resolution as a whole, it also voted for a number of the hostile amendments. Two key amendments for which India voted affirmatively cast a particularly troubling light on the government’s fidelity to the Constitution.
Amendment L 75 reads: Reiterating the importance of respecting regional, cultural and religious value systems as well as particularities in considering human rights; while amendment
L 76 reads: Underlining that fundamental importance of respecting the relevant domestic debates at the national level on matters associated with historical, cultural, social and religious sensitivities.
These amendments seek to undo the international consensus that cultural sensitivity must always yield to the duty of all states to protect universal human rights as embodied in the Vienna Declaration and Programme of Action. This deference to cultural and religious value systems is particularly problematic in the Indian context as it reinforces casteist practices and gender discrimination, not to mention discrimination on grounds of sexual orientation and gender identity. An unqualified deference to cultural and religious value systems is also antithetical to the Indian constitutional framework.
The freedom of religion clause in the constitution (Article 25) is specifically subjected to the limitations imposed by the other fundamental rights. This is because the constitution accommodates the concerns of women members of the Constituent Assembly, such as Hansa Mehta, who talked about how the freedom of religion could well become the tyranny of religion, especially over women.
Similarly the practice of untouchability is at heart a cultural practice undergirded by a religious value system. This practice was declared a constitutional crime under Article 17. What the criminalisation of the practice of untouchability indicates is that the Indian Constitution is no passive supporter of culture and tradition. Rather, the Constitution prohibits cultural practices that violate fundamental rights.
When India voted for these amendments, it shows a profound lack of respect for the Constitution and its values. 
The Indian abstention did scant justice to the way the conversation on LGBT rights had evolved domestically. From being a fringe issue, it had become a matter of widespread concern as reflected in social movement positions, media coverage as well as the fact that major political parties were supportive of LGBT rights including the largest opposition party the Congress. This emerging base of solid support however did not embolden the government to play a leadership role and India preferred to be non committal in its vote.
From another perspective, India’s abstention could be seen as at least not as regressive as the previous position. In 2015, India under the current Modi administration, joined Russia, Pakistan, Saudi Arabia, China and Iran to vote against the extension of same-sex partner benefits to employees of the United Nations. If that vote is taken as the benchmark, India has moved from a ‘no’ to an ‘abstention’.
The fact that India abstained instead of voting no in 2016, can be attributed to the fear of negative media coverage which would tarnish the governments international image. The overall position of the Indian government evolved from a no vote in 2015 to an abstention in 2016 because of the fear of negative publicity of the no vote in 2015 and the desire of the current Indian administration to avoid the same. It is also an indirect tribute to the strength of the national level campaign to decriminalise LGBT lives mounted vigorously by LGBT groups along with media, civil society and academia.
Suresh Kumar Koushal v. Naz Foundation, (2014) I SCC 1.
17. Abolition of Untouchability.—“Untouchability’’ is abolished and its practice in any form is forbidden. The enforcement of any disability arising out of “Untouchability’’ shall be an offence punishable in accordance with law.