There is one circumstance under which you can do something like

3dttest++ -setA FILE1 -setB FILE2

and that is when the 2 files each contain multiple volumes. That may be what you did in the earlier case.

However, AFNI error messages pre-suppose that you understand what you are doing, and the messages are designed to help you patch up simple errors. It is a major error on a user's part to run a data analysis program without understanding (at least in outline) what it is doing -- this one "good" way to do junk science. Treating complex software as a black box that gives beautiful answers is a very very bad idea. That kind of attitude has led, for example, to improper design and construction of nuclear power plants that had to be shut down and fixed at enormous cost.