Comment 2 for bug 32589

This also happens for non-special locations that can't be shown in the side pane tree. E.g., if you configure nautilus not to show hidden files (which also hides hidden dirs) and then enter a hidden dir the previous dir isn't deselected in the side pane tree.
Hiding are re-showing the side pane "fixes" this (well, actually it always deselects the dir even if it shouldn't, so it's actually another bug, but one that works well together with this bug).