So what are they complaining about?

Some things matter more than others. And this is important. But I would suggest that The Scotsman is displaying a basic lack of numeracy here:

"ALMOST half of all drinks served in Scottish pubs are short measures, according to an investigation by trading standards officials.
Only one in ten tipples sold during the survey was accurate. It also found that 43 per cent of drinks were over-poured, prompting concern among alcohol campaigners...
Officials visited 193 pubs across Scotland, buying 343 drinks between 31 July and 18 August. Only 39 were sold correctly, with 155 - or 48 per cent - found to be short and 148 too large."

If I buy a fifth of a gill of whisky in a pub, and if the amount of liquid in the glass is measured accurately to - say - a level of three decimal points of a gill, it is overwhelmingly inevitable that the measure will either be over or under a fifth of a gill. If the barman is honest, one would expect the probability of an over-measurement to be roughly the same as that of an under-measurement. This is precisely what the above survey shows: 43% to 48%.

Accordingly, on the basis of this survey, to declare emphatically that almost half the drinks sold are short measures is ludicrous. And then to complain that most of the other half are over-measures is equally daft. Unless The Scotsman tells us the degree of accuracy used to measure the drinks in the survey and the extent of the variance, the article tells us very little.