There are methods to fold liners to achieve the flush look. Basically, all edges should be above water level. Only drains and window cutouts require some form of leak protection (usually mechanical clamping with flanges and/or bolts).
Koi forums and a few above ground pond builds on MFK has good info. Even Neo had a thread years ago on a liner build.
Hope you find the leak. Just be aware that the water pressure will pull the liner down as you fill. So more leaks may develop. Final tacking of the top edge of the liner is usually done with the tank 2/3 full. Bulkheads already installed maybe an issue.
Thanks for the information. Yes, we didn't tack the liner down up top except with some clamps to hold it in place. We did intentionally leave some slack in the liner where the bulkheads were installed... but maybe that wasn't enough. Ill look into other liner builds.. I haven't seen all that many though.... Thanks