It would be fairly difficult for the agent to do. They need to receipt the money for trust account reconciliation and the auditors would pick it up pretty quickly. Also something would show up on your end of month statement. The also must provide a ledger/ receipt to the tenant on request so they would have to show the rent they paid.
It would be too difficult for the agent to try and skim unless they were collecting the rent by cash into the office.
You could ask for a copy of tenant ledger from the agent and post it to the tenant asking them if the rent receipted is actually the rent being paid.
If you can't trust your agent get a new one, otherwise you will be worrying the whole time about everything they do. You don't need the stress.