@JbrinkZA First comment WHY would you want a port between the CISCO and the MIKROTIK that is a hybrid port.
This makes ZERO sense to me. Just simply carry both over as vlans in a trunk port and then on the MIKROTIK you can deal out vlans as required.
Please explain the purpose of a hybrid port between two “SMART” devices (both acting as switches).???
@Durango, not sure where you get info but for bridge vlan filtering, this is the best guidance.
http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1