We bumped into something like this at a subset of sites after upgrading from MX16.X to MX18.X earlier this year.
At the most problematic site, it turned out that the upstream ISP modem had its DHCPv6 server enabled, with a 15 minute lifetime. Every 15 minutes, that lease would renew, and that would cause the MX to drop 1-3 packets.
This was the same issue at the other sites that were affected, though the DHCPv6 server was handing out longer leases at those locations. Disabling that feature on the ISP modem was the resolution for this.