Simon and Elias' ever-evolving relationship in their Quantico days, despite Simon's faking being gay, culminating in a heartfelt goodbye kiss from, surprisingly, Simon, that felt a little more than friendly.
Caleb and Will's Odd Friendship has a lot of homoerotic overtones, what with Will being all to happy to help Caleb re-infiltrate the cult that he used to belong to.
In Season 2, Sebastian and Harry circle each other until finally Sebastian gives in and kisses Harry in LCFLUTTER.
The series deliberately plays up Alex and Shelby's friendship during their days at Quantico to the point where Alex at one point asks if they're acting a bit too chummy with each other... in order to create a contrast with the present, where it turns out that they've had a serious falling-out.
To the point that some people would much rather see Alex/Shelby as opposed to the canon Alex/Ryan and Shelby/Caleb.
After Nimah becomes Alex's new roommate, they have the occasional friendly moment, most notably in "Guilty", where Alex can be seen apparently bussing Nimah's cheek while the gang is out having drinks.
While for most of her screentime, Hannah really doesn't like or trust Alex, their interactions in "Inside" - the episode in which they met - seem very flirtatious, with Hannah repeatedly calling Alex beautiful.
Alex: If it wasn't an open bar already, I would totally ask to buy you a drink.
Hannah: And I would say yes, please, and right away.
In the second-season premiere, Alex has dinner with Ryan and Shelby, and says that Shelby will be keeping her company while Ryan is off on a mission for several months. When Alex is forced to leave early, she kisses both Ryan and Shelby good night.
Shelby is Alex's handler, and upon meeting Alex she comforts Alex when Alex relates that she doesn't like learning how to lie, cheat and manipulate in the CIA.
Shelby and Nimah have their share of moments, from working together in the past timeline to Shelby telling Nimah that the latter is one of the few people in the world Shelby loves.