FFMPEG comes to mind immediately as an example. Essentially, you call ffmpeg to convert media1 with specs and provide media2 as an output for it. I'm mostly understanding and accepting that this ordering matters, because you're applying arguments onto the input instead of trying to do something on the output for some reason.
Where it gets confusing, though, is if you want to resize and crop an image for example. You may end up with different results depending on the order you specify these operations.
Maybe this particular use case makes sense because resizing and cropping hard-coded coordinates could be confusing. However, other operations that seem like they shouldn't interfere with each other sometimes do.
It would be nice to see some type of handling so there isn't this type of confusion. Perhaps some type of --override command, otherwise default to a consistent output regardless of order.
In contrast, I can't think of any issue I've had with "ls". I like that -l -a -t -r can be combined into -latr, but it does make learning the terminal very confusing for beginners when this isn't always supported or consistent in other programs.