I'd like to ask which preposition is correct in the following sentence:
The number of employees on/in collection points depends on quantity of raw cotton necessary for production.
Probably. There are likely to be two things - collection points at which the pickers deliver the cotton and processing stations where it goes into the processing system.
For the latter, you would be quite correct to say that there were personnel on the processing stations.
It is the same as saying the receptionist on the front desk or the clerk on the payout counter.