I also find I can't select an opponent's ship unless I have autoturn off and wait until the end of the turn. Even then, sometimes it does not stay selected long enough for me to be sure it even was selected.
Here is why Ted may have thought he was the only one having the problem: I for one, and I suspect everyone else, did not really think we should be able to select the ship of another civ. Why should we. We can't move it or make it attack, or anything. Of course, it would be nice to be able to gather some information about the ship if I were planning to attack it or thought it might be about to attack me, such as, how damaged is it? What are its strengths (HP, def, etc.)? Essentially, when I found out how I could successfully select an alien ship, I thought I was taking advantage of a bug of a different nature. Now I tend to agree with Ted. We SHOULD be able to probe an alien ship with our sensors. The simplest way of doing this is to let us select the ship.