Problem solve.
In Cisco Switch you cannot add an Access port to a Trunk port, instead you need to create a native Vlan and add the Vlan to the Trunk configuration.
This is the correct way:
interface GigabitEthernet2/0/38
switchport trunk allowed vlan 3,99
switchport trunk encapsulation dot1q
switchport trunk native vlan 3
switchport mode trunk
end
Regards