take the kids into custody?

They were waiting for Katie to come home so they could bring them all in at once. Under normal circumstances that team of red hats would've been more than enough to secure the location and not have to worry - they WERE just kids after all - so why the urgent need to transport them? Having them there would be an excellent way to convince Katie to surrender peacefully. If she tries fighting back or puts a gun to her own head so they can't take her alive, they'd tell her that if she goes ahead and does that her kids are going straight to the Factory. But if she gives herself up maybe they end up in her sister's custody in the green zone instead. Up to her.

They weren't expecting a special forces style assault on the safe house. But as we saw in that episode where the Red Hand hit the recruitment center, a few of the red hats are ex-cops but most are just average shmucks who probably get a few weeks' worth of training before they hit the streets. Against a guy like Broussard they're completely out of their depth.

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I feel like a legitimate complaint about this show is that it kind of sets up these crises and then solves them fairly quickly (same or next episode). But because the crises are easily resolved, it makes them seem kind of phony and the people involved not terribly credible.

And it often comes off feeling like filler, cycles of nonsense activity done to keep the "occupation" premise going and not do any serious science fiction.