She can bring the case to the kantor Wilayah, well before even thinking about a lawsuit to PTUN.
If she is in Mataram then this is the Kantor Wilayah NTB which is in charge. She has to look for the Divisi Keimigrasian Subbidang lalu Lintas Keimigrasian. She should go there and explain why she feels the decision is unfair.
Kanwil is in charge of supervising Kantor Imigrasi and the fact that they correctly apply the law. They don't like to go against the Kantor Imigrasi and may try to find excuses not to, but if your friend is assertive enough, she may get her point heard. Let me explain you why.
One thing is interesting in what you posted. it's this:
It doesn't sound right or fair to me as all her documents were in order the reasons given to her were ridiculous. The immigration officer told her that they are worried she would be taken in another country and trafficked!
(...)
My question is what to do next? She's already been told she can't have her file back for at least 30 days!
The "30 days" bit makes me think that she may get her point heard and that the excuses KanIm gave won't stand scrutinity by the KanWil.
First, it is a urban legend to say that Imigrasi can refuse a passport because they
think that human trafficking may be at play. If they can prove it, then they can refuse the issuance of a passport.
Thinking is not enough and they have absolutely no right to deny a passport because they
think whatever.
They fully know it and this is why they haven't issued a
surat penolokan which would be the correct procedure. They just express their refusal verbally and they are smart telling your friend that she can't get her file back before 30 days. Reason is simple:
When one applies for a passport, one has 30 (thirty) days to bring all documents, do the interview, . give his/her fingerprints and get his/her picture taken, pay the fee...etc. If one doesn't complete the procedure in 30 days then the application is automatically rejected.
Now, if Imigrasi would have a serious and LEGAL reason to refuse the passport, they would have issued straight away a
surat penolakan and they would have had 1 day (not 30) to give back all documents to the applicant.
Imigrasi gives this excuse of 30 days so that the application get automatically rejected and that they do not have to give any LEGAL reason, something they obviously don't have. At the end of the 30 days they will issue internally a BAP, stating that the applicant didn't bring/didn't have all documents and no-one will ask any further question to them.
This is why I tell you that your friend may get her point across IF she is confident and assertive. Obviously not an easy task for an Indonesian girl, probably young, since it means standing against authority but if she wants her rights respected, she has good chance to have a positive result. She will need your support.