Information
ESXi does not use the concept of native VLAN. Frames with VLAN specified in the port group will have a tag, but frames with VLAN not specified in the port group are not tagged and therefore will end up as belonging to the native VLAN of the physical switch.
For example, frames on VLAN 1 from a Cisco physical switch will be untagged, because this is considered as the native VLAN. However, frames from ESXi specified as VLAN 1 will be tagged with a '1'; therefore, traffic from ESXi that is destined for the native VLAN will not be correctly routed (because it is tagged with a '1' instead of being untagged), and traffic from the physical switch coming from the native VLAN will not be visible (because it is not tagged).
If the ESXi virtual switch port group uses the native VLAN ID, traffic from those VMs will not be visible to the native VLAN on the switch because the switch is expecting untagged traffic.
Solution
From the vSphere Client, select the ESXi host and go to Configure >> Networking >> Virtual switches.
Highlight the port group where VLAN ID is set to native VLAN ID and click Edit settings (dots).
Change the VLAN ID to a non-native VLAN and click 'OK'.
or
From a PowerCLI command prompt while connected to the ESXi host, run the following command:
Get-VirtualPortGroup -Name 'portgroup name' | Set-VirtualPortGroup -VLanId 'New VLAN#'