I'd need to see a save, but it's highly unlikely this is erroneous -- multiple people have reported this sort of thing, and it's always cloaked ships of some variety so far. If you look at the intel summary on the galaxy map, it will tell you what kinds of ships are there. When you detonated the tachyon missile, it revealed that other ship and so the tractor beam was able to suddenly grab it. Before that point, the tractor beam could not grab it because it was cloaked.
It's always possible there is an error in there somewhere, but I have yet to see one with this specific subject.