Yo, my favorite system writing error is whenever a system can give skills for a resource, but then the author makes it too easy to get said resources and just stop mentioning the skills, it always makes me laugh.
In all seriousness though, I find systems annoying because writers often use it as a crutch and few of them actually explore it in any meaningful way. Like you said, I know there are some that do it well, but I've seen so many bad ones that I get reluctant when I see the system tag. Personally, when I find a system novel I do like it usually because, A, they have the system as part of the setting that everyone has AND actually makes the mc work in the rules of said setting, B, have the system come with a MEANINGFUL price, C, has the system be sentient and function as a duo protagonist, or D, is a particularly interesting system. Some examples are Death and Me which is a mix of B and C, Illumination a naruto story which is B, Tree of Aeon which is A, Absolute Great Teacher which is D, and Wake of the Ravager which is all of the above. Now these novels differ quite a bit in terms of quality, but the system aspect, at least, I feel they all handled quite well and made it actually benefit the story.