The best you could do is compare the expected flow each step, based on group voting ticket, against the actual flow, and make sure the total difference does not exceed the number of below the line votes.
Edit: Antony green has an estimate used in his calculator. "At Federal election, around 95% of mainland voters, and 80% of Tasmanian voters, fill in their ballot paper using the group ticket ('above the line') voting option."
http://www.abc.net.au/elections/federal/2007/calculator/sena...
With the number of candidates doubling last election, Tasmania was probably more like 90%.
http://blogs.abc.net.au/antonygreen/2013/08/record-number-of...
However in extremely close races, such as what happened in WA - it can come down to very small numbers of individual ballots and how their preferences are stated, as to what order senators are elected in.
This then affects the re-flow of preferences.
[1] http://results.aec.gov.au/17496/Website/SenateResultsMenu-17...
[2] http://results.aec.gov.au/17496/Website/External/SenateState...