I have a network with exactly this setup - 2 sets of 2xC9500-48Y4C with Meraki monitoring.
I've had very rare intermittent issues with monitoring alarms and incorrect warnings on the dashboard but nothing that has stuck around long enough to be worth troubleshooting.
I'd just suggest confirming:
- Your upstream router has the correct firewall ruleset mapped to the IP address the Catalysts are for the Meraki connection. Double check the destination/ports against what is listed in the dashboard (help -> firewall info)
- SSL inspection is disabled on the upstream firewall.