"A window is over a table" should in principle work, and you should report it. But be warned that "There is a window above the table" is a better translation; your translation would be closer to "Окно над столом" - it informs us about the location of a window rather than what's above the table. The difference is not too crucial in this case (particularly since you used "a window" rather than "the window") , but you should educate yourself about the information contained in the Russian word order: https://www.duolingo.com/comment/13955228
Can Над столом окно also mean "the window is on the table". I know that there might not be might be many situations to say this, but I imagined a situation where 2 construction workers talk with each other and they are talking about a window that is not placed in a wall (just the component lying on a table).