While plants themselves typically won’t cause a hole in the liner, their root systems can be quite opportunistic. If there is even smallest, slightest hole where water is slowly leaking or weeping through, plant roots will often find it. Over time, those roots will enlarge the hole as they grow through it.
We've observed that certain plants, like bamboo, can actually puncture the liner. For this reason, we generally avoid planting bamboo near water features.