Usually, the drain is just sandwiching the old tub and the new liner together to make the seal. Water could get between them either from there if the sandwich isn't tight enough, or maybe from the overflow if the liner and tub aren't sandwiched tight there. So, loosening the drain basket should allow it to drain. The stagnet water might be pretty raunchy. As to how to prevent it from happening, that's tougher. Not sure how flexible the liner is, whether they glued it to the tub there with maybe some silicon, and didn't get it perfect, or were just relying on the compression from the drain to sandwich it together and seal.