Payroll reimbursements showing as "net pay" rather than separately

Hello all, 

I am needing some help with reimbursing expenses to employees. 

I am bookkeeping for a small construction company. Employees pay for materials out of pocket and then are reimbursed. I followed Keith L's method (https://www.sagecity.com/ca/sage_50_accounting_ca/b/sage_50_ca_supporthub_blog/posts/how-to-reimburse-an-employee-purchase-through-payroll) and created reimbursement options through the payroll function. The expenses go straight to the linked accounts and are not taxed, which is great. So far so good.

However, on one of the printed pay slips I realized that Sage 50 is adding all the amounts together and considering it all as "pay" -- for example, the pay slip is stating that year to date net pay for Employee X is $1,500 when in actuality it is $1,200 and $300 reimbursements. But it doesn't make that distinction.

Is this just a superficial error on the document or will this create problems down the line when I am trying to create T4s? The reimbursements should not be considered income, as far as I know. 

Is there a different, better way to calculate reimbursements?

Thank you for your help!