Trying to pick fights with every single person you've worked with so far is not really what I would call very forward-thinking.
In truth, all Naru really cares about at the company is her own image, and fuck anything that might make her look bad.
Except she's so singlemindedly obsessed with it that she kinda loses sight of what would actually make her look good.
So far, she just feels annoyed with Nene's "casual" way of getting in the team, which can be understood considering Nene's reason to get into programming is "hey, it looked fun !" and it really looks like she got in because she's friends with Umiko. And with Hajime, it doesn't feel like she has any actual beef with her, just doesn't like the fact she keep have her redo her task over and over again instead of taking the time to properly plan it, risking her to look bad for not keeping up deadlines and thus putting her future employement at risk.
Naru sees an issue with the planing and game design that have a considerable impact on her work, she brings that issue up to talk about it, I don't really see an issue with that, except that her tone could be a little more gentle, yeah, but aside from that, she's not wrong, in my opinion. Sure, she could just shut up, be a nice little kohai and do as she's told, but then she'll miss the deadline and somebody with a much higher rank than Hajime would come and ask why she took ages to do that mini-game. At this point, either she'll take the blame and not get employed or she point out Hajime's fault and it's her that might get in trouble, especially if she didn't clean up her act by then. With that takl, Hajime did find out her way of doing things could be improve and already started with improving. In the long run, Naru bringin that issue up is certainly a positive thing.
And really, when you're in need of a job and have the opportunity to work in a field and place that interest you, you don't want to see that chance gone just because someone else doesn't do her job properly.