The problem is simple: They were used in the wrong manner. That's all there is to it.

Those are sidebars not toolbars there's no discussing about it. Using icons from a folder that's meant for toolbars, menus (contextual, drop downs) and buttons (which I don't approve of by the way) is just wrong and can cause this. As far as I'm aware there wasn't a set of guidelines like we do have now and as a result things like this happened. Icons from the wrong category were used because they worked, it's not a problem with Breeze or a problem with any other icon theme, it's a problem of the software.

The only thing that has to happen is for software that uses this layout to use 32px icons which seems the most reasonable size and use icons from only one category. These are windows for preferences it only makes sense that they use icons that:

Have a prefix to their name like preferences-x-y

Or

That have a more generic prefix like kdialog-x-y

Instead of pulling icons that have no place there.