The following contains spoilers for episodes 1-3 of NieR Automata Ver1.1a, now streaming on Crunchyroll.
Whether it's Nier and Kaine, or 9S and 2B, the NieR franchise has always included subtle hints to potential romance. Though it's not a major plot point, fans are always eager to speculate if their two favorite characters have chemistry.
Sometimes it's confirmed that at least one character has feelings for the other; one example is when Nier kisses Kaine during Ending C of NieR: Replicant. In NieR: Automata's case, 9S's mannerisms towards 2B imply a massive crush. Though 2B is a lot more stoic and is less open about her feelings, (similar to Kaine) there leaves more explicit implications that she might like him back.
Their History
2B and 9S have a history of partnership - and therefore a lot of experience, at least on 2B's side. 9S seemingly either doesn't possess memories of 2B, or has very little recollection of them. But every time they meet, they are able to form a close bond.
9S always develops an attachment first, whenever he introduces himself and will try to show off his knowledge; as seen in episode 1, when he's narrating machine behavior. 2B however seems to keep him at arm's length - but from what we saw in the first scene, she's carrying his body, so this could be that she's just afraid of attachment. To add on, in episode 2, she tells 9S how his voice puts her at ease.
Her Tone
Every time 9S and 2B are reintroduced, 9S always addresses her with honorifics and uses polite speech. But 2B always tells him that honorifics are unnecessary, and uses casual speech. In Japanese, unless you know someone really well, people don't withhold honorifics with another person - even close friends will still sometimes use honorifics, lovers included. Though it's also common for those in an intimate relationship to withhold honorifics as well. In professional or work-related settings, polite speech is a must - and 2B and 9S are in a colleague relationship, after all.
Lovers Suicide
2B's mannerisms aren't only what hints at how she potentially feels. The way the setting is framed and the choices the animators make during their interactions, can serve just as much exposition. At the end of episode 1, when 9S realizes he won't survive from his wounds, the pair decide to sacrifice themselves via black box. The way they hold onto each other and the framing of the scene, is reminiscent of that of a lovers' final moments. You could even look at them pulling out their black boxes (which the animators put a heavy emphasis on) as 2B and 9S showing each other their hearts. In classic romantic tragedy literature, lovers exchange words of affirmation before their deaths. Knowing Yoko Taro's penchant for symbolism and tragedy, this could very well be what is happening.
Hidden In Plain Sight
The OP and ED also offer some insight on their relationship. At the end of the OP, we see 2B leaning down to meet 9S, and lifting her hands up to cup his face. Game veterans will know that this is before she strangles him, but it's portrayed in an intimate setting, flowers (namely Lunar Tears) and all. And at the end of the ED, 2B leaves her sword behind to run to 9S, who's excitedly waiting for her. What's more, her blindfold comes off, which is against the regulations of YoRHa - so it's almost like they're eloping.