Hello,
if you want to remove the subinterfaces and the Vlans, configure the below:
Device#conf t
Device(config)#no interface GigabitEthernet0/2.50
Device(config)#no interface GigabitEthernet0/2.90
Device(config)#no vlan 50
Device(config)#no vlan 90
Is there any up/up port configured for Vlan 99 ? Post the full running configuration of the device...