You just overdischarged them below what those lipos will tolerate. Don't blame on the lipos, you are pretty much the reason. I suspect you overdischarged the other one as well. Overdischarge will cause the swelling or puffing you've seen. Some lipos will tolerate lower voltage better than others, I use 3.4v/cell as a cutoff for just this reason. Plane guys use an even higher cutoff.
You could have easily had a fire with the one you left plugged in and turned on. I'm glad you didn't hurt anyone else.