You need to target the error codes from https://docs.wso2.com/display/AM260/Error+Handling and update it to your custom JSON messages. For auth token related errors try modify _auth_failure_handler_ as below:
<sequence name="_auth_failure_handler_" xmlns="http://ws.apache.org/ns/synapse">
<property name="error_message_type" value="application/json"/>
<filter source="get-property('ERROR_CODE')" regex="405">
<then>
<sequence key="converter"/>
<drop/>
</then>
<else>
</else>
</filter>
<filter source="get-property('ERROR_CODE')" regex="900901">
<then>
<sequence key="invalidCredential"/>
<drop/>
</then>
<else>
</else>
</filter>
<filter source="get-property('ERROR_CODE')" regex="900902">
<then>
<sequence key="missingCredential"/>
<drop/>
</then>
<else>
</else>
</filter>
<sequence key="_cors_request_handler_"/>
For your case Invalid Credential has a 900901 code , so it will match and need to define invalidCredential.xml as below :
<?xml version="1.0" encoding="UTF-8"?>
<sequence xmlns="http://ws.apache.org/ns/synapse" name="invalidCredential">
<payloadFactory media-type="json">
<format>{ "req_id": "REQ_ENT_1356985018299_9678", "err_resp": { "code": "28001", "msg": "Invalid access token" } </format>
<!--Add your custom message and format here. This will be your output-->
</payloadFactory>
<property name="RESPONSE" value="true"/>
<header name="To" action="remove"/>
<property name="HTTP_SC" value="401" scope="axis2"/>
<property name="messageType" value="application/json" scope="axis2"/>
<send/>
</sequence>