is scope insensitivity really a brain error?

One way to look at this is to pick questions where you're really sure that the two versions of the question should have different answers. For example, questions where the answer is a probability rather than a subjective value. One study some years ago asked some people for the probability that Assad's regime would fall in the next 3 months, and others for the probability that Assad's regime would fall in the next 6 months. As described in the book Superforecasting, non-superforecasters gave essentially identical answers to these two questions (40% and 41%, respectively). So it seems like they were making some sort of error by not taking into account the size of the duration. (Superforecasters gave different answers, 15% and 24%, which did take the duration into account pretty well.)

It seems to me that this is bordering on saying that persons who made a different choice to yours are therefore not just wrong, but suffering from something, their brain is not working properly and they need to be taught how to make better choices. where "better" obviously means, more in line with the choice you would make.

It's not about the choice in isolation, it's the mismatch between stated goals and actions. If someone says they want to save money, and they spend tens of hours of their time to avoid a $5 expense when there was a $500 expense they could have avoided with the same effort, then they aren't doing the best thing for their stated goal. Scope-insensitivity problems like this are very common, because quantifying and comparing things is a skill that not everyone has; this causes a huge amount of wasted resources and effort. That doesn't mean everything that looks like an example of scope insensitivity actually is one; people may have other, unstated goals. In the classic study with birds and oil ponds, for example, people might spend a little money to make themself look good to the experimenter.

(I would also note that, while the classic birds-and-oil-ponds example study is often used as an illustrative example, most peoples' belief that scope insensitivity exists and is a problem does not rely on that example, and other examples are easy to find.)

This article (open access) provides a useful summary of scope insensitivity as a phenomenon that is well researched and seems robust:

https://www.sciencedirect.com/science/article/pii/S2211368114000795

I would caveat that the primary data reported has almost no evidentiary value because of the smalls ample size (n = 41).

I feel that you have a separate issue beyond the existence of scope insensitivity as a phenomenon, and that is that Yudkowsky committed a value judgement when he labelled the phenomenon a production of systematic error. The article linked above describes how scope insensitivity differs from an unbiased utilitarian perspective on aid and concern (it is this latter approach that Yudkowsky would presumably consider correct):

In the specific case of valuations underlying public policy decisions, one would expect that each individual life at risk should be given the same consideration and value, which is a moral principle to which most individuals in western countries would probably agree to. Nonetheless, intuitive tradeoffs and the limits of moral intuitions underlying scope insensitivity in lifesaving contexts can often lead to non-normative and irrational valuations (Reyna & Casillas, 2009).

scope insensitivity would only be irrational if saving birds were the only criteria in play. to save more birds, give more money. but this is almost never the case

The question was designed to isolate those two factors. You can claim the respondents all had secret, rational reasons to answer the way they did, but there's no evidence of that, and you haven't even proposed what those reasons could be.