Troubleshooting Payroll Issues in Alpaca Health

This article covers the most common payroll issues you may encounter in Alpaca Health and how to resolve them.

Worker Not Included in Payroll / Missing Pay Rates

If a worker is flagged as missing from payroll or you receive an "Action Required: Workers Missing Pay Rates" email, it typically means one or more pay rate types have not been configured for that worker. Common missing rates include:

• Drive Time rate – required if the worker has any drive time appointments

• Admin rate – required if the worker has approved admin hours

• Clinical/Training rate – required for billable or training sessions

To fix this, navigate to your Payroll Settings → Pay Rates and configure the appropriate rate for the worker. If the pay period has already closed and you cannot edit the rate yourself, contact support@alpacahealth.io and provide the worker's name, the rate type, and the dollar amount.

Note: Pay rate changes apply to the current payroll period going forward. If a rate is added after the period has already started, it may need to be manually applied by the support team to cover the current period.

Worker Flagged with "Zero Rate with Hours"

The system automatically flags any approved appointment type that has hours but no corresponding pay rate. If you do not intend to pay a worker for a particular appointment type (e.g., a lunch break or an appointment type you don't compensate), you should either:

• Change the appointment type to one that has a rate assigned, or

• Cancel or remove the appointment entirely to exclude it from payroll

Hours in Payroll Don't Match the Schedule

Alpaca Health calculates payroll based on when session notes are signed and verified, not the date of service. The schedule view displays sessions by date of service, which can cause a discrepancy between what you see on the schedule and what appears in the payroll or finances tab.

For example, if a session took place on the 16th but the note was not signed until the 19th (after the payroll cutoff), it will appear in the next payroll period, not the current one.

The payroll cutoff is typically end of day on Sunday (three days after the pay period ends). Any notes signed after this deadline will roll into the following payroll period.

Session Payrolled at the Wrong Pay Rate

If a session is being paid at an incorrect rate (for example, a billable session being paid at the drive time rate), you can correct this by updating the appointment type or pay code on the session. If the payroll period has already been finalized, contact support for a manual correction.

When creating or editing a non-billable event in the calendar, make sure the Pay Code Type dropdown matches the intended pay type. The Pay Code Type is what determines the pay rate — the optional secondary dropdown under the client name is informational only and does not affect pay calculations.

Incorrect Session Billing Code Affecting Payroll

If a session was logged with the wrong billing code (e.g., a drive time code instead of a clinical code), you should:

1. Delete the incorrectly coded appointment (if it has not yet been submitted to the payer).

2. Create a new appointment with the correct billing code.

3. Start the session, add notes, and sign it before the payroll deadline.

If the session has already been submitted to the payer, contact support to file a claim correction. Provide the correct billing code and session times.

Admin/Non-Billable Hours Not Appearing in Payroll

Only approved admin, training, or other non-billable hours will appear in payroll. Hours that are pending or rejected will not be included. An admin user must approve these hours before they will show up in the payroll tab.

Late Notes and Off-Cycle Payroll

If a session note is signed after the payroll cutoff deadline, it will automatically roll into the next payroll period. If you need to ensure a late-signed session is paid in the current period, contact support as soon as possible — the team may be able to run an off-cycle payroll to cover it.

Incorrect Pay Amount / Underpayment or Overpayment

If a worker was paid at the wrong rate and payroll has already been finalized:

• Overpayment: You can add a deduction equal to the overpayment amount to the worker's next paycheck using the Add Deduction button in the payroll dashboard.

• Underpayment: You can add the owed amount as a bonus or additional pay entry using the Add Pay Entry button for the next pay period. Note that adding pay entries may be restricted after the payroll processing deadline for the current period — contact support if you are unable to add an entry.

Paying Yourself as a Practice Owner

If you are the practice owner and want to pay yourself through Alpaca Health, you must configure a pay rate for yourself just like any other worker. If you prefer to pay yourself outside of Alpaca, you can ask support to exclude you from the payroll run. Revenue from your sessions will still be deposited to your business bank account, and you can review payout details in the Finances page.

Drive Time vs. Travel Time Pay Codes

Alpaca Health has a dedicated Drive Time pay code that allows you to set a separate rate for drive time, distinct from the admin rate. If you do not want a separate drive time rate, you can either:

• Change the appointment's pay code to Non-clinical, or

• Set the worker's Drive Time rate to be the same as their Admin rate in the employee's pay rate settings.

Still Need Help?

If you are unable to resolve a payroll issue on your own, contact the Alpaca Health support team at support@alpacahealth.io. When reaching out, please include the worker's name, the pay period in question, and a description of the discrepancy so the team can assist you quickly.