There were three things that didn't ring true in this. As you point out, her troops must surely have been a bit suspicious of her trances and in only being interested in seeking out human collaborators rather pushing forward the fight. I don't see how the 14th Virginia can only be made up of inexperienced young boys who follow their leader's poor decsions without question. They would have had to fight hard in order to have survived to have arrived at the Naval base.
The second was when the 2nd Mass. first discovered the base. They were quite right to be very suspicious but then that very quickly subsided. I thought it was very strange that they had never picked them up on the radio and yet had picked up militia in Africa. Now an explanation for that did come a bit later on, but even that explanation was a bit odd, so why didn't they ask the question straight away?
The third was how convenient it is to boost the numbers of the 2nd Mass. and to find a huge arsenal of weapons just at the point they will need them to push on Washington D.C. And Katie had to be someone Dan knew too.
The Court Martial scene was good, but there seems to be a lot of people they are meeting who are forgetting who the real enemy is. What the Court Martial did point out was the shear unbelievability of the ridiculous storylines we have had in the previous Season. Quite honestly, I don't believe their story either. Either that, or Tom Mason really is the smartest person left on the planet and clearly deserves to be the next President just like Pope said.
Where is Pope and his gang anyway?
And why did Tom keep secret Cochise and the Espheni communication device when they were quite willing to give away very important details of the rest of their future plans? And given that Katie apparently knows all this anyway, one would have to ask how she knows, and then we don't need to be shown an image of an Overlord in order to make the connection.
Also, Dan's long game of getting Cochise and Dingaan to come to the rescue isn't going to work if Katie already knows about them. Still there is a lot else going on. Isabella and Maggie are free now, and Maggie doesn't seem to have lost any strength with the loss of her spikes. Now we know why she had to lose them so quickly. If she had still had them when Ben had one removed her's would have been lighting up the base.
And a final thing; why can't Ben detect the Overlord? Is that why he had to have a spike removed? If Katie is being controlled by it then Ben should know about it.