You are right that by default all inbound traffic is allowed (which is the largest drawback of Meraki in my mind. If you want to make sure that your business-partners can't access just everything, you need a different device which is typically an additional ASA in my case).
You don't say anything about your setup so this is only a wild guess, but it is very often overlooked:
You are using IKEv2 and you have multiple subnets configured. The first established subnets work, but your AD controller is on the additional subnet which is not working. This would be an additional drawback of the Meraki MX as this is quite often incompatible to other vendors:
https://documentation.meraki.com/MX/Site-to-site_VPN/IKEv1_and_IKEv2_for_non-Meraki_VPN_Peers_Compar...
If you found this post helpful, please give it Kudos. If my answer solves your problem, please click Accept as Solution so others can benefit from it.