YShahar
Enthusiastic duct-tape engineer
I know it's a bit late for the tears you already have, but we learned to use a scrap piece of liner or underlayment to drag big stones around. Number one, it's easier because you can create a "handle" of sorts and number two - you avoid scraping rock on liner if you're moving them into place. (My hands still hurt thinking about how heavy some of those stones were!)
Yes, whenever I'm able to rope my Larger Half into helping me move rocks, we use the underlayment-as-rock-sling trick. When working alone, if I have to roll rocks I normally wrap them up in underlayment. I think what happened with this one is that I moved it into place thinking that there was underlayment under it when there wasn't. And yeah, it's one of those rocks that I shouldn't have been moving at all as a one-person job--but then, I get impatient to get things done...
The rocks that I was pin-wheeling into place when I discovered the leak were outside of the liner--part of the landscaping around the stream--so at least I didn't compound the damage. But now I'm totally paranoid that there are all kinds of pin-hole leaks all over my stream... I started digging out gravel and spot checking that the underlayment is in place under the rocks. So far, it seems to be fine.