I have income on my T4A in box 048 and 028, but I cannot enter both in the same form. Why is this?

Box 48 is used for Self-Employment. Since that income requires additional entries in the Business/Self-employment section of your return, the issuer of the slip should not have included non-self-employment boxes on the slip. Contact the slip provider to ensure both boxes are accurate and if so, request 2 separate T4A slips.