When entering into a new arena one has to expect a certain amout of problems. I have had my share of experiences which mirror yours. I had an ESC suck the life out of one of my 6S batteries causing it too puff up. I've had ESCs catch on fire and motors seize up. I think the brushless systems ARE getting better for the 1/8 scales but the manufacturers shouldn't do their R&D with funds from our pockets.
The short answer to your question is yes a faulty ESC can damage your LiPo by sucking the life out of it or going dead short and allowing the battery to transfer its capacity as quickly as possible. However, with the absence of physical damage, which you didn't mention (puffing) I tend to believe that the batteries connections may be bad after heating up and possibly desoldering themselves. You might want to peel back the covering on your LiPo a bit to check them out.