There is a clear training problem in science. But I believe part of it is that the knowledge on how to write good software is stuck in companies. You can't learn it in school either. I keep hearong about companies that have to make their new hires unlearn what they learned in class... So where would scientists learn good practices? (in my experience books arent the answer either)

I don't think it is primarily a problem in training. It is a problem in incentive. For the most part, scientific software is written to fulfil a goal, and usually that goal is in order to publish a paper. Paper publication is what scientists are judged on, not the quality of the software they write. The software only needs to work well enough to get the paper published. Once the paper is published, all incentive to maintain or improve the software disappears, especially if the message of the paper is primarily the results obtained using the software, because then all of the citations will be referring to those results, not the software.

There are two main exceptions to this rule. One is when an actual software engineer ends up working as a scientist and having to write papers (like me). Then, the paper is more likely to be about the software itself, and the citations of the paper are from people who have also used the same software. This creates an incentive to make the software high quality, in order to get those citations. The other exception is when an institute decides that the world needs a decent piece of software to fulfil a vital role, and actually funds its development.

Oh, I should probably mention - I just helped out with a programming course for undergraduate medical science students. Most of the time I was tearing my hair out about the terrible programming practices being taught by the module leader, who admittedly had absolutely no computer science qualifications whatsoever (and in fact didn't know the difference between a forward slash and a backslash).

I think a solution to this is to recognise software quality as a common benefit, and divert funding towards it, allowing real software engineers to have an actual meaningful career in university. Universities are usually all over common benefit stuff, so you would have thought this would be easy enough. The Research Software Engineer programme in the UK is a start.