Well technically mizuho said herself, the reason she's with Ena because Ena love her not the other way round. I think even before that convsation with her little sister, Ena probably has notice it. It's a one sided love.
Ena on the other hand love Mizuho and the kind that do whatever she feels like - example, she kiss Mizuho right infront of her little sister eventhought they just met, agreed to crashed at mizuho's sister house ( surely it must be mizuho, the one suggested) or to suddenly buy a necklace for her girlfriend. Which I find it normal if you're in love with someone. But knowing the feeling is not mutual can be a burden.
So something like Mizuho not worried about her girlfriend went missing probably a big deal for Ena. She probably hope that Mizuho be a bit worried about her and go out to find her. But she didn't! So it can be emotional for Ena.
Another thing, it's Mizuho who suggest to go to work seperately. So Ena's uneasiness is completely understandable.
Oh well it's just what understand. I might be totally wrong.
