Ah, I see. So perhaps it wasn't bugged, then, just unfamiliar.as it looks on your screenshot, the "target" panel is active. You have to actively switch over there to see the subtarget, as it is with normal npc targets, too. It is not like when you scan structures or megaships, where the subtargets appear in the contact list. It is more a subsystem than a target.
Also, you need to be close enough to be able to target the limpet dock port, if you get too far away, you lose target tracking completely. The best approach is having subsystems on a keybind, and flipping to the subtarget as soon as the scan finishes, instead of fiddling with the panels.
In any case, I only had seconds to consider what to do, because my ship exploded a few moments later anyway