The election commission had rejected 77 of the 4,851 ballot papers during counting for the presidential elections last week. Of these, 21 had been voted by parliamentarians and 56 by state legislators. Mr Kovind, who took over as the country's 14th President on Tuesday, had won with over 65 per cent of the vote share against opposition's Meira Kumar.
BJP leaders say most of these 21 invalid votes - often disqualified because of an extra dot or inverted comma - too would have otherwise gone increase NDA candidate Ram Nath Kovind's winning margin.
Election agents - who witnessed the counting - have told the BJP leadership that many of the votes declared invalid for such errors had voted President Kovind.
It was a secret ballot and the party can't identify lawmakers who demonstrated what the party believes was a less-than-serious attitude towards voting in the presidential election.
He said what had also riled PM Modi was that the party had done everything within its control to ensure that the lawmakers do not make a mistake, right down to a special video demonstration for them just a day earlier.
NDA's nominee M Venkaiah Naidu is pitted against the Opposition candidate Gopalkrishna Gandhi in the vice presidential polls.
The government estimates that vice presidential candidate has the support of around 550 MPs in the electoral college of 787 lawmakers from the Rajya Sabha and Lok Sabha. And like Mr Kovind, can easily win. But from the government's perspective, the election process was important more in terms of the margin than the outcome.
Get the latest election news, live updates and election schedule for Lok Sabha Elections 2019 on ndtv.com/elections. Like us on Facebook or follow us on Twitter and Instagram for updates from each of the 543 parliamentary seats for the 2019 Indian general elections.