The problem of the lightly used railways was not that the report had inconsistencies, the problem was that there was not enough traffic to justify the number of railway lines open in Britain. The line from Thetford to Swaffham is reported as having 9 passengers on each of the 12 trains per day. Geleneagles to Comrie is reported to have had 5 passengers on 20 trains per day.
What is remarkable is that by 1963 when the report was published BTC/BR had already shut 3429 miles of railway since 1948 so the passenger numbers/freight totals on those must have been really really poor. After the Beeching report BR only shut another 3633 miles of railway up till 1970 when closures more or less stopped.
I don't think that really lets Beeching off the hook.
For someone who took a decidedly mathematical approach, it seems entirely reasonable to criticise some of the methods used, such as assuming so many people would "railhead" to the nearest mainline station, or justifying the case for closure by discounting the revenue of end to end passengers where a less direct route existed.