First of all, 5th coloumn.
1. Secret groups don't act like that. Everybody knowing everybody is not a good idea. Neither is everybody knowing every detail of the plans.
2. You don't take in people who just mention they want in. And you don't letthem in on all the plans and introduce everybody.
3. You don't put all your eggs in one basket. Using same place as communication centre, weapons storage, sleeping quarters and interrogation room is not a good idea.
4. Vs are aliens. Remember that. They may dislike their leaders but they are different species. Their species surviving will take precendes over everything.
The only reason they were not wiped out within days is that Vs match their stupidity
1.1. Once you learn your leader is about to be assassinated you get her out ASAP. You don't have her stand just inside shuttle with ramp down.
1.2. It's also not a good idea for her to be walking around in the open later
2. You have cameras that can fit within a ribbon of cloth but don't intall them in critical parts ofyour ship, such as soldier breeding room, blue energy batteries storage....
3. Once you start suspecting peopleare on to something or are vocal in their opposition you place them under surveilance.
Few other things I noticed:
-Vs became aware of humans once we detonated our first nuclear bomb (1945). Ignoring the fact how they were able to spot it from any great distance and distinguish from simialr processes in stars they arrived within few years (V whose body is discovered laterdies), established large enough network of people to both gather information and cover for each other so that by early 1990s they were able to start experiments on human genome and knew enough to actully pull them off.
-Once Vs started to move among people openly (S1) nobody figured that since they look like humans they could have done that already
-Having a huge command centre under Manhattan? Right under one a V ship? why not use some military base in the middle of nowhere?