How exactly do you “see” it? Using /tool sniffer or using some action=log or log=yes firewall rule?
I would suspect most a firewall rule in chain input of /ip firewall filter to drop the ICMP echo request packets. Packets decapsulated from IPsec transport ones inherit the in-interface attribute from the transport ones, so if you drop anything coming from WAN except connection-state=established,related, this could be the explanation.
If the above is not sufficient, post the complete configuration of mtik3, following the hint in my automatic signature below.