As of season 2 and the movie, Perrine's over the crush.
Don't forget the way Sanya always finds her way into Eila's bed after her night shift—and how Eila is in obvious adoration of Sanya. "Doesn't it make your heart throb?" indeed.
Heck, in an interview, the creator even described their relationship as "basically a junior high school boy who is hesitant on how to tell the girl he loves how he feels". Can't get more blunt than that.
Even more, in the "What If" series of tweets, we have Sanya's case:
She was afforded the liberty of obtaining long-term leave or even to step down from the front lines if she so wished, but instead after she met briefly with her parents she returned to the night sky. The sky which her beloved flew in.
Let's not forget Minna's feelings for Mio, either.
Based on the events in Episode 8, Minna probably transferred her feelings for her old boyfriend (including concern for his safety) to Mio.
There's also a lot of Les Yay between Mio and Yoshika, what with Yoshika admiring Mio like crazy and Mio's mentor/Cool Big Sis role for Yoshika. The frequent Say My Name moments between them don't help.
And then of course theirs Gertrude and her sister Chris. I know some may argue that it's just a sisterly love, but given some of tone she takes in regards to talking about her little sister, plus the fact that their real life counterparts were married... I think it's safe to assume, (as a good number of Gertrude Fan's agree) that Trudey is a major sis-con.
The fandom is starting to notice this on Perrine and Lucchini. Many of their interactions are rather amusing in terms that they're complete polar opposites, especially episode 9 of the second season, where they share tons of Ship Tease moments, which would lead the popularity of this couple.