Same thing's happening to my Bridge, but it's not a problem with intruders. If intruders had planted a magical re-exploding bomb, my officers would be long dead by now. My bridge keeps falling to 50%, but doesn't take any items to repair. After the 5th time, I got fed up and told my engineers to stop. I checked its health again, and it instantly repaired.
All this began happening after my Chief Engineer reached 35% AI, which is when he starts auto-assigning people to repair stuff. That might mean something. I don't know if it's a glitch or if the CE just gets bored and blows stuff up, but it seems useless since the systems somehow repair themselves and don't take anything to repair... =/
Edit: Oh, found another thread with the same question: <http://www.3000ad.com/forum/index.php?showtopic=2001442&pid=18528&mode=threaded&start=#entry18528>. It looks like it's all the CE's fault. If you're carrying upgrades, he will go on a mad repairing spree. Just get rid of the parts or upgrade them