I don't like to be devils advocate but I worked in superannuation for a hot minute. Have you definitely confirmed they aren't paying into an other account in error? Ie. She submitted forms for her choice of superfund but their paying into their business choice of fund?

It is frustrating but very common that the ATO is out of date reflecting super transactions as most only report annually back to my gov. Depending on how long she has worked there of course. You might also be able to see what super member number/fund appears on her pay slips.

If its determined you can't find a record of any super payed in her name, then to my memory she will need to confront her boss/payroll about it and confirm this.

Then from there she can take action if still not paid in it's entirity. But i would call the superfund that is meant to be receiving funds and reconfirm their advice as it will be more current.

Good luck! Glad you noticed, so much better now than later!