Police say that the reason for Junaid Khan's murder - in which his three siblings were also injured by the knife-wielding mob - was mainly because of a row over seat space on the train.
But a man arrested for being part of the mob said on TV that he was goaded into it by others because Muslims ate beef.
Shaqir, one of the surviving brothers, told reporters in the hospital that the attackers "flung our skull caps, pulled my brother's beard, slapped us, and taunted us about eating beef".
Under Narendra Modi's Hindu nationalist BJP, the cow has become a polarising animal and religious divisions are widening. Restrictions on the sale and slaughter of cows are fanning confusion and vigilantism.
Two years ago, a mob killed farm worker Mohammed Akhlaq over "rumours" that his family had stored and eaten beef.
Vigilante cow protection groups, operating with impunity, have killed people for transporting cattle. Muslim men have been lynched by Hindu mobs, mostly in BJP-ruled states, for allegedly storing beef and, in one case, for helping an mixed-faith couple elope.
Many are wondering whether India is hurtling towards a "mobocracy" under Mr Modi's watch. They also question the prime minister's silence over the killings.
There is a sense of a rapid breakdown of law and order when it comes to protecting minorities.
The police at the railway station in BJP-ruled Haryana failed to save the teenager on Friday. The local police station chief told The Times of India newspaper that they could not rescue the boy because of the crowd.
"Such things happen. Whenever there is a riot or fight such things happen and people say some communal things but we can't do anything," he said.
The chief minister of BJP-ruled Rajasthan, where 55-year-old dairy farmer Pehlu Khan was lynched in April, offered condolences over his "demise" without mentioning the fact that he had been murdered. A BJP lawmaker said he had "no regret" over the killing because Khan was a "cow-smuggler".
The spate of mob murders is earning a bad name both for Hinduism and Mr Modi's government.
"India is slipping beyond the pale. It is unfathomable that the ancient Hindu horror at the taking of life, any life - the very same doctrine of ahimsa, or non-violence, that governed the beliefs of men like Mahatma Gandhi and the Rev Dr Martin Luther King Jr - should in our time be used as a justification for murder," noted author Aatish Taseer, writing in The New York Times.
The Economist magazine has suggested that under Mr Modi debate about communal relations has "atrophied".
But India's senior most bureaucrat in charge of law and order, Rajiv Mehrishi, has instead accused the media of "over reporting" the incidents.
"I don't think it [hate crime] is new in India. It is feudal in nature. Today, they shake the conscience. You cannot say lynching or hate crimes are something new. I think they are over hyped and over reported," he said.
To be sure, hate crimes are not new to India. The crisis of violence is not unique to the country either - many point to the US, where there are high rates of gun crime.
And mob lynching is also not new to India. Hundreds of people - more than 630 between 1982 and 1984 alone - were murdered by mobs during the three-decade-long Communist rule in West Bengal. The reckless vigilantism was blamed in part on political oppression and appalling law and order. Interestingly, there was little public outrage.
On the day of Junaid Khan's killing, a Muslim police officer was beaten to death by a Muslim mob outside the main mosque in Srinagar, the summer capital of Indian-administered Kashmir.
Earlier this month a Muslim activist was allegedly murdered by overzealous government officials after he objected to them taking pictures of women defecating in the open.
India has a shambolic record when it comes to religious violence. It ranks fourth worst in the world for religious intolerance, according to a recent Pew Research Centre analysis.
Women are routinely branded as witches and lynched to death for property in large parts of the country. There are also high rates of domestic violence.
But the problem with Mr Modi's government, say many, is that it is seen as ineffective - or unwilling - to rein in the thuggish Hindu mobs.
It is, in the words of sociologist Shiv Visvanathan, a "politics of insecurity and anxiety" which is leading to anarchy even as the "state watches lynching as a spectacle".
Many wonder whether India is staring into a dangerous abyss when a government with a majority led by a powerful leader refuses to condemn hate crimes and a vast number of citizens stay silent or appear to privately support it.
A lawyer tweeted that he had "family elders supporting [the lynchings]. Took me great self-control to avoid anger".
Why is there a lack of outrage outside a handful of journalists, teachers and activists? Have most Indians become inured to violence and intolerance?
On Wednesday, countrywide protests are being planned against such "targeted" murders.
What many Indians who choose to remain silent do not realise is that small-scale and large-scale violence are intimately connected. The perpetuation of hate crimes can easily lead to wider violence.
"Every act of violence that you tolerate without protest, brings it a step closer to your doorstep. It is because small violence is tolerated that big violence is rendered possible," writes Sudipta Kaviraj from Columbia University.
It is a warning India ignores again and again.
On Thursday a 15-year-old Muslim boy, returning home from Eid shopping with his three brothers, was killed in a brutal assault by a mob of about 20 men on a train in the north Indian state of Haryana.