Okay, so have I had this problem before? Yes. Let’s go, Anecdote Time With Ellory!
A while back, I was writing a short story/attempt at a novel. I had three main characters, all girls: [name_m]Clayton[/name_m], [name_u]Quincy[/name_u], and [name_f]Naomi[/name_f]. [name_m]Clayton[/name_m] an [name_u]Quincy[/name_u] are obviously masculine, while [name_f]Naomi[/name_f] is very flowery and feminine. Then, another time. I named my cast: Thorton (f), [name_u]Jackie[/name_u] (f), [name_u]Sam[/name_u] (m), and Thomaston (m). These are all masculine. NOW, my MC’s names are in alphabetical order (how did I do this??): [name_m]Bradford[/name_m], [name_u]Connelly[/name_u], and [name_m]Damien[/name_m]. They all sound somewhat masculine, yet [name_u]Connelly[/name_u] is a girl. So yeah, almost all of my names match.
HOWEVER, I don’t see this as a problem, especially depending on the number of people in your cast. By a general rule, dystopian and fantasy and sci-fi–all of that–has bigger casts, more world building as opposed to more realistic novels. Like seriously. Off the top of your head, count how many [name_u]Harry[/name_u] [name_m]Potter[/name_m] characters you can think of. And since you’re writing sci-fi, it shouldn’t be a big deal. Think how many characters are in “big” YA sci-fi/dystopian, like Hunger Games and Divergent. Sometimes it helps to look in the “rules” of your genre. Ex: [name_f]Katniss[/name_f] and Peeta can both be associated with foods (even if Peeta’s spelled wrong, but don’t rain on my parade!), but no one complains about that. (They might just complain that [name_f]Katniss[/name_f] should’ve ended up with [name_u]Gale[/name_u], but that’s another story for another time.)
I feel like those names won’t seem as obvious, if lost in a cast of larger characters. For example (even though I don’t write the aforementioned genres), along with the more unisex [name_u]Connelly[/name_u], I have more feminine [name_f]Vera[/name_f], [name_f]Charlotte[/name_f], [name_f]Imogene[/name_f], and [name_f]Jacqueline[/name_f].
Now, if those two characters were like MAIN CHARACTERS, then yeah, there might be some problems. If they are in a sort of relationship together (like best friends, romantically involved, or enemies), then this would be more obvious (Like my Thomaston and Thorton. [name_f]Do[/name_f] you know how similar those names sound? That’s why Thomaston went by the nn [name_m]Tom[/name_m]). Also, if every character had a place name, this would be obvious. Additionally, “[name_m]Dutch[/name_m]” isn’t really a place, you know? It’s actually a language, or a people, while [name_f]Scotland[/name_f] is a place. And, if [name_f]Scotland[/name_f] is called [name_u]Scotty[/name_u] the majority of the time, then the connection won’t be as obvious. Now, if her name was Scottish, then…
Point is: Nicknames can be a lifesaver, sometimes!
And also: it’s okay to have filler names. That’s what Find and Replace is for. Call [name_m]Dutch[/name_m] “[name_m]Dutch[/name_m]” as long as you want, and, if you decide to change it, then do that. That’s the beauty of technology. Unless you write longhand. Then, there might be problems…
AND MY LAST POINT: Think in real life. People have matchy names sometimes. I mean, I have two friends with the names [name_f]Emma[/name_f], and they were friends. I know two Rileys that are friends, and the same with two Avas. [name_m]Just[/name_m] be creative, and, at the end of the day, get opinions from beta readers and such.
It’s all going to be fine. You got this.