I work two jobs, both are casual, and I am claiming the tax free threshold from one job. Each time I am paid from the other job (the one I am not claiming the tax free threshold from), my employer withholds a different amount of tax per working day, anywhere between $80 and $125 per day. I am wondering how my employer determines how much tax to withhold each pay period since it seems to be done completely randomly.
Likely the answer is : They do what they are told. Most employers do not run employee tax calculations - they hire a company to do it. Unless you are really large, doing those calculations yourself is stupid - there are liability issues that an external firm has to handle via their insurance. Also there possibly are a lot of regulations and updates, so unless you are in the business of writing this software or providing this service, you are just running a minefield of things you can do wrong.
The more detailed answer is: they follow the law. Likely it depends only on your income of the day, with some extras in case. There are rules (not even guidelines) for this, and the software that is used (no one does that by hand) just follows them.
They actually are published, i.e. https://www.ato.gov.au/calculators-and-tools/tax-withheld-calculator/
In your primary job you claimed the tax free threshold. in your secondary job, you would have informed them you have 2 jobs.
The first job is taxed from the tax free threshold, the second job is taxed at the highest threshold, to ensure you pay enough total tax between the 2 jobs and don't receive a debt when you do your tax return. the extra tax paid will be refunded to you.
For example if you earned $30k at each job you would be in the first and 2nd bracket individually. but with a total of $60k, every dollar above $37000 should actually be taxed at the 3rd bracket! (32.5%)
$0 – $18,200 0% $18,201 – $37,000 19% $37,001 – $90,000 32.5%