Surplus and loss is usually just that a clerk can't account for the difference between what money they have and what money they should have. There is usually a way to account for pretty much everything else (including 'money left on counter'). The discrepancy could be as simple as not giving out the right change at some point during the day, or might even just be a typo (entering £5.10 on the shift sheet instead of £5.15 for example).
At the value of train tickets I'd completely agree.
The old methods for finding differences are the best - to this day I'm astounded by how many differences turn out to be transpositions!
90p short? Has £4.50 been input as £5.40?
£2.34 over? Has £12.60 been input as £10.26?
(The trick is, if your difference divides by 9 to a whole number (you may want to think in "hundreds of pence") then your difference is likely to be an entry which contains the correct digits, just in the incorrect order.)