I have the same problem on Nemo. More specifically, I had made a small app that displayed files of a directory in alphabetical order, and then when I look at it in Nemo it isn't the same order because I didn't implement their smart algorithm.
I fail to see how this is a "problem"? You implemented a sorting mechanism that was useful to your application, while Nemo implemented another which as this thread demonstrates seems to be much more useful and intuitive for the average user. This is also of course not specific to Nemo, as no 'modern' file manager on Linux sorts filenames like it's 1980 and all you are able to feasibly do is step through the bytes.
