When I am run tracert 192.168.12.1 from server, it goes outside of VPN and if IP is 192.168.3.1, it works correctly (see attached)
I can’t understand what’s wrong.
P.s 192.168.3.0/24 is also connected with VPN at same router.
Please export and attach the configurations for both units so that we can see the exact setup you are using (I’ve assumed they are both MikroTik units).
On router 1: /export hide-sensitive file=Router1
and
On router 2: /export hide-sensitive file=Router2
you should check your export file and replace your Public IPs, DDNS, Private Key. IPsec Secret, Custom ports.
Then yes you are secure.
use notpad+ for EZ replacement in all lines.