I arrested someone and called the Prisoner Transport. The transport showed up but the officers just pointed their guns at the person I arrested and they just went around randomly and not back to the car. And I can't call another prisoner transport because the other one hasn't gone. Please help!

Does this happen all the time? If not, it's normal. Usually the backup you called calls for another unit who will arrest the suspect instead.

I think if you call a prisoner transport, LCPDFR only allows the prisoner to be placed into the prisoner transport vehicle, and sometimes there may be cars blocking the way to the vehicle, so the pathing system gets messed up. If you stop one of the people randomly running away from cops on the street (but not arrest them), the cop chasing after the criminal will usually load him into any nearby police car (including your's).