In other scenes, there are various references to this invisible-to-all-but-their-defenders thing. Why is no one else getting their own army ready? If a town has 50 warriors ready to defend their homeland, wouldn't you assume they'd be ready to protect it? Or is that thing in Japan? Was this thing a big fake out? Is the Japan government just getting in their own bad books by failing to act on this supposed global crisis? What is the WLF going to do about the giant military machinery in Japan? We don't know. In a plotline as small as "what is happening to all the people", these loose ends seem ridiculous. They shouldn't have spent any time on this "event" when the point of the game was to finish Joel's quest.
That giant island thing is mentioned over and over again, but never answered. The entire subplot of rescuing a giant lady floating in the sky? It should have come up much earlier in the game. Why were the same soldiers who rescued Ellie in chapter 1 doing this? They have to know the only chance of success is the same people from the opening section. And why is the video being shown on television in every bar they go to? Is it there in the name of public awareness? Do they think the government is going to care about this anyway? They could've done better than this boring cliché. I don't think the player cares.
Ellie and Jesse still kiss after almost having sex, with their phones on the bedside table (there are some nice visuals here). Are they getting back together? This wouldn't make sense, as the context seems to suggest they're no longer a couple.
As if having them kiss was not disturbing enough, they end up in bed together a few chapters later. Yes, another whole day passes without anything happening between them.
The last fight scene with Nathan was annoying and rushed. They just seem to run around, hitting every pillar and boulder that's there. It's quite clear they were planning this fight all along, yet we only see it happen a few hours after