I don't know if this is truly a bug per se, but it's non-intuitive behavior that I think should be changed.
When you select an object with one of the Marquee tools, you can move the selection around independent of the pixels that are selected. If you want to move the pixels, you have to switch to the Move tool.
But if you use Free Transform on the selection, then immediately after the transformation, Photoshop acts like the Move tool is selected when the Marquee tool is still selected. i.e., you can no longer move the selection independent of the pixels until you make a new selection. Photoshop should respect the function of the selected tool at all times.