GP leaders and practices have said omissions being punished would have been accommodated by PCTs, and area teams' hardline approach was a cost-cutting exercise.
GP reported in October that patients at Gordon House Surgery in Ealing, west London, had spoken out after a £12,000 PPG payment was withheld because the practice failed to put a link on its website.
Other practices have reported similar experiences, and GP leaders say the problem is widespread.
Medical director for Londonwide LMCs Dr Tony Grewal said several appeals in London had been rejected. NHS England was applying the 'absolute letter of the law', he said.
South London GP Dr James Heathcoate said his practice lost more than £12,000 because it used a patient-friendly, edited version of the PPG report on its website, rather than publishing the full document.
'In the past, people would have had some flexibility,' he said. 'NHS England doesn't have the capacity to interact with practices on a one-to-one level.'
One west London practice lost about £4,000 because it published the PPG report online late, despite having completed the DES work.
A GP at another west London practice said NHS England was not interested in complaints, after the area team took back £11,000 for missing a deadline to upload the PPG report - a charge the practice denies.
'We've done over and above what we needed to,' the GP said. 'But it is not interested. It's about trying to claw money back from GPs.'
Dr Grewal said it was a 'new reality' for practices. 'It is within their remit to refuse to pay on a technicality and they seem very happy to do that.'
LMC leaders in other parts of England report similar concerns. Essex LMC chief executive Dr Brian Balmer said there had been a number of apparently 'arbitrary' decisions.
Wessex LMC chief executive Dr Nigel Watson said a number of practices had payments withheld and were turned down at appeal. 'They've refused to pay, even when practices can show they've done the work.'
GPC deputy chairman Dr Richard Vautrey said area teams' 'more remote' relationship with practices was partly to blame, but 'clearly NHS England is looking for savings'.
An NHS England spokeswoman said the PPG DES was assessed against published criteria and GPs could dispute decisions. For 2013/14 there will be a unified approach across London.