Dear Neha,
As you have asked about the apprentice advisor, I don't know about Delhi where its office is, but I am in Noida, and our apprentice advisor sits in Kanpur.
It is your internal matter as you are deducting PF if the salary is more than 6500. There is a problem if you deduct their PF now; it will be deducted on how much salary because you have not done any bifurcation. So, you will now deduct on 6500, but when you will absorb them, their basic should not be less than 6500.
If the stipend will be less than 10k, then the ESI Act will also be applicable.
As you have mentioned that trainees are not shown on the payroll register, and a separate sheet is made for them. Now the question comes: how and where are you booking their amount in the balance sheet? If you are not booking their salary in the balance sheet and paying off the record, then during PF/ESI inspection, you will not be caught. However, things are, of course, illegal.
Thanks,
J S Malik