Here's an example of an interface that I consider to be poorly designed; it's from the software FileTouch. This package allows one to set different date fields on a file to arbitrary dates.
The main reason I consider this a bad design is that it is cluttered and oriented contrary to the usual flow of use. To illustrate this latter point, consider the order in which I usually find myself using this interface:
The obvious first step in using a tool like this is to select the files upon which to work and we see that this one control is where we would expect it, in the upper-left corner. However, since it's simpler to drag and drop a group of files onto the icon than to open another browse window and find them, my initial view is as reflected here: file selection is the zeroth step because it's already been done when the tool opens.
The other numbered steps reflect my usual order of use. As you can see it's in the opposite direction to the layout of the controls. It's possible that others may use this differently but I have only my own, frequent usage by which to judge this and the layout seems backwards based on this. Also, I suspect that my own pattern of use is not unusual. For one thing, the large block of controls for changing file attributes interrupts the usage flow for the unique feature of this tool - changing file dates and times - with a feature easily accomplished by standard (Windows) tools.