Hak and Jae-Ha. The latter's initial admiration of Hak can be quite easily interpreted as a crush. This, combined with the notably close friendship that develops later sets the stage for some fans to ship them.
In the manga, when the gang needs to cross a rickety bridge to leave Kouka, Jae-Ha mentions if the bridge collapses, the only ones he's saving are Yona...and Yoon, while stepping over Hak in the process. It seems like he's taken one too many Hak rejections and has decided to go after the shota instead.
...and then he saves Kija anyway.
Soo-won and Hak. Hak takes Soo-won's betrayal much, much more personally than Yona does, and the two of them were endlessly admiring of each other in the past. Yona mentions in an aside that they even raised Soo-won's pet falcon together.
Yun is everyone's mom, but the way he nags Zeno to help with the chores, stop acting like a kid, and take better care of his clothes makes him sound more like a particularly irate wife.
The fanbook doesn't help matters: on the relationship chart, Yoon's feelings towards Zeno are summed up by tsundere-like "stop making me worry!", while Zeno's towards Yoon are that Yoon "has him by his stomach," a line frequently used to describe how a woman attracts a man with her cooking.
Female x Female
Yona and Lili in the manga, though very one-sided (from Lili's side that is).
Lili kissed Yona (on the forehead, but still), potentially confirming that she loves her.
Lili says Yun-Ho is so cute that she would marry her.
Ayura and Tetora come across as being very close, almost romantic at times. They even shared a quite intimate Headbutt of Love before splitting up with the Happy Hungry Bunch to save Lili and Yona from a Sei slave camp.
