Frankly "scrutinize it" is not the whole story for why the programme motion was defeated. According to the Guardian:
The rebellion against the programme motion was led by the former Tory chancellor Philip Hammond, and one of Johnson’s leadership rivals, Rory Stewart. They were keen to secure reassurances that if the government had not succeeded in negotiating a free trade agreement with the EU27 by the end of 2020, the UK would not leave without a deal.
Hammond told the Times the bill was “a camouflage to a no-deal Brexit at the end of 2020”. Stewart, another of the 21 Tories who had the party whip withdrawn last month, said he and some of his fellow rebels had negotiated through the night to give parliament more control over the next phase of the Brexit negotiations, including being able to vote for an extension to the talks.
So apparently it was also a tactical vote to get some concessions from the government on the future negotiations with the EU. It's not clear to me what is the exact form of those concessions sought, whether they are/were a "gentlemen's agreement" or in some legislative form, e.g. amending the bill.
Hammond has explained his position in more detail in an article in the Evening Standard yesterday:
On Saturday, the Prime Minister gave a commitment to include in the Bill the so-called Nandy-Snell amendments that the previous government accepted, giving Parliament control over the negotiating mandate for, and the final form of, the future relationship. The Prime Minister’s commitment is indeed welcome but it needs to deliver Nandy-Snell in substance, not just in name. With the UK-wide backstop gone, the default position, if agreement is not reached, will be WTO terms — effectively no-deal. And those of us who have campaigned against no-deal in 2019 are not going to watch it be sneaked in through the back door in 2020. [...]
I hope the Government’s Bill will be given a second reading in the House of Commons today. But for it to deliver an acceptable outcome for ALL the people of the UK it will need big amendments in committee to ensure that it is the first step on the road to an ambitious future trade partnership, not a blind leap into the abyss of a no-deal future.
The government gave some verbal assurances today through the justice secretary, Robert Buckland, but apparently these were not enough for the expelled Tories.
As per discussion in the comments, although this Hammond situation has been described by some of the British press press as a tactical thing, probably the concept of vote trading is more relevant; in this case the trade having failed to happen.