A possible solution to this problem is to add a travel reimbursement processing fee to the budget that will be charged each time patient travel must be reimbursed. Some sponsors may not be able to accept overhead on the actual item, but may be able to accept a processing fee. Another option would be to increase the coordinator fee in the per-patient budget to account for this activity.
If overhead is mandatory at your institution, then we recommend sending the sponsor the institution-wide overhead documentation. We work with several institutions that have their research overhead published online and the link can be easily provided to the sponsor/CRO.