I am absolutely certain it is a translation issue, but I am not certain about your theory (or your quoted percentage) that it is because the dev's native language doesn't use gender pronouns, for 2 main reasons: 1, the error is very infrequent (so much that the only reason I even commented was as a partial joke and comparison to the daughter's use of parental names instead of their title) and would likely happen more often if your proposal were correct. And 2: I am unsure of the percentage of worldwide languages but I do know of at least 10 languages from major countries(countries with global economic infrastructure to the point that their languages are fairly recognisable around the world) myself (and these are just the ones I know of, I am sure there are more) where not only do they use gender specific pronouns, but their nouns are also gender specific. Having said all of that, the translation confusion isn't that big of a thing for me, as I said I only mentioned it as a funny comparison.
It happens decently often in the game, actually. I'm not going to count instances, but I remember a number of these mix-ups before v0.3 or even v0.2. I think there are two easy explanations. Maybe the dev mostly understands but still makes some mistakes. By way of example, English speakers self-overcorrect the "and I" construction, which is an incredibly easy one; something more complicated, like understanding gender in pronouns when it's completely foreign to your language, is probably more prone to errors. (You can see a similar problem with native speakers of Asiatic languages who try to use prepositions in English; our prepositional use is often actually pretty inconsistent, so mistakes are understandable and even likely.)
Another possibility is that the dev is using an inferior translation tool / service, in which case the translator itself could be flawed and cause the problems we've seen. It's hard to know, and I'm not saying this is for sure the problem. But these are plausible explanations and are decently likely.
Your mention of knowing a lot of countries that have gendered pronouns is neither here nor there. The existence of gender in some languages doesn't even remotely mean that all languages have them. I gave you at least three languages as examples; you can easily Google to see the stats and find articles about non-gendered languages. That's roughly akin to a nomadic desert tribe claiming there are no trees in the world because they don't have any wherever they roam. It has literally no bearing on the existence of trees. And just because many languages with gendered pronouns are widespread doesn't mean someone not natively speaking them necessarily has a good grasp on using gendered pronouns.
I do agree that it's noticeable and a little funny to see, given what we ourselves know. I'm pretty sure Nightaku is using a poor translation utility for the English script. It could definitely use improvement, but I'm fairly lenient on this type of thing. I just find it hard when I can't actually understand what's meant, like in examples I've previously given.