This is more of a warning than a question. I have just completed two large Meraki MS deployments. In one we had to integrate Merakis on a legacy Cisco Catalyst infrastructure where only some Catalyst switches were being replaced. Many were remaining.
Issues:
Our native VLAN was configured for VLAN ID 5 on both sides of the trunk. MS350 on one side, Catalyst 3750 and 3850s on the other.
Cisco Catalyst switch reported a VLAN ID mismatch for 3 of 8 allowed VLANs
This caused the trunk to be blocked for those VLANs on that single trunk (meaning only one trunk from that switch existed to the network and it was blocking for those vlans)
The only fix was turning on "spanning-tree bpdufilter enable" or turning spanning-tree off.
I am surprised that I have not seen more people complaining about this.
In the other deployment where I had a mostly homogeneous Meraki network, I still had to disable spanning tree on the port to our ISP uplink and make sure our MDF stack was root or we saw all kinds of wonky behavior.
So my warning is, if you are seeing issues that dont make sense, check Spanning-tree...