The Audit Script for deploying Malwarebytes as a Custom App (which is linked to this support article) is looking for a top-level PayloadIdentifier ("com.malwarebytes.tcc") when it checks to see if Malwarebytes_Protection_profile_general.mobileconfig exists locally before installing the app. This PayloadIdentifier is now modified by Kandji during deployment, so the audit script can't find this profile using this method.
line 60 of the script needs to be changed from
PROFILE_PAYLOAD_ID_PREFIXES=("com.malwarebytes.tcc" "io.kandji.mwbnotifications")
to something that looks for a different PayloadIdentifier in that profile, such as (as just one possible example):
PROFILE_PAYLOAD_ID_PREFIXES=("com.apple.TCC.configuration-profile-policy.E18E6763-E6D5" "io.kandji.mwbnotifications")