If you are in a directory, and have selected a file, then try to right click on another file or the directory you get a "Cut,Copy,Remove" menu instead of the standard "Refresh, Hide Menu..." menu. This makes normal right clicking a two-step process. You have to first left click, then right click to get the desired menu.
Seems there's more to this one than I thought, drag and drop is also broken in the same manner. 1. Select one file with left click. 2. Select and hold a second file with left click and drag this somewhere. 3. Both files are selected when only the second should be. The above behaviour should only occur when Ctrl (or shift) is held down. You can work around it by left clicking the second file once, then clicking and dragging again, but I don't think this is a good way to work.
The first bug mentioned is solved in 4.o and HEAD branches: the only way to select multiple files with button 3 is to hold down the control key while clicking. The second detail mentioned is a different story altogether. It is the behaviour added in 4.0.1 which allows you to drag a multiple row selection without holding down the control key. Yes, it does imply that if you already have something selected and only want to drag one row, you must click on the row, release, then click again to start the drag. Many fm's work this way.