So, had a call with Checkpoint this morning and we could resolve the issue!
To explain why the error happended a short info about our setup.
Our endpoint protection will reach the AD Domain Controller through a public IP on another FW and there we're doing a NAT to the DC.
On the endpoint protection server in the Organization scanner I entered the public IP, not a hostname. Therefore we saw an error in the log on the EP about the public IP not being a SAN inside the certificate we installed on the EP server.
I then added a host definition inside clish on the EP server:
add host name fqdn.from.domaincontroller ipv4-address pub.lic.ip.address
The pub.lic.ip.address is the IP address on the firewall where we're doing the NAT.
After that, I had to enter the hostname instead of the public IP address in the Organization Scanner settings.