While Ms Miller accepted she had bought the slices after discounting them, the sale itself had been carried out by a team leader, which was tacit approval of the transaction.
The team leader had not said anything to Ms Miller at the time, despite being able to refuse to sell her the goods, and had only raised the issue with Mr Wilson later.
The policy around buying discounted goods was unclear and had never been put in writing, the authority said.
Ms Miller had offered to pay back the $5 price difference, but that was not grounds to infer she had acted dishonestly.
The authority also found the allegation of disrupting other staff was not serious enough to justify dismissal.
It also cleared Ms Miller of alleged misconduct for failing to turn up for a rostered Saturday shift.
Ms Miller had agreed to work on Saturdays only on a trial basis and, when she found the shifts too difficult due to childcare commitments, she let Mr Wilson know in writing.
Mr Wilson insisted the Saturday shifts were not a trial and told Ms Miller she had to work them.
He tried to make other arrangements but when he could not sort anything out, he would not attend mediation over the issue.
Authority member David Appleton found the shifts were on a trial basis only, and Mr Wilson's refusal to attend mediation was a breach of good faith.
He ordered the cafe to pay a $2500 penalty to Ms Miller.
Mr Appleton also found the cafe was unjustified in dismissing Ms Miller, and ordered it to pay $6191.50 in lost wages and $8000 in compensation for humiliation, loss of dignity and hurt feelings.
Costs were reserved.