I came across similar NIC ordering issue some time ago. When I added more than 4 vmxnet3 adapters to the machine, FreeBSD numbered interfaces differently in comparison to VM ethernet adapter order, that issue is described here. When I used E1000 interfaces, the problem disappeared. I had to use workaround script that renamed vmx interfaces in FreeBSD based on their mac address, so that interface order was the same on VM and FreeBSD.
This is however something different. I'm not touching interfaces on the VM, I'm just unassigning/disabling interfaces in pfSense GUI under Interfaces -> Assignments. Though it definitely bears some similarity with aforementioned NIC order bug (meaning that everything is fine with only 4 interfaces on the machine).