The transporter has always been a story problem in that it can be a magical problem solver in one episode or movie, that is forgotten about when a similar dilemma comes up. One reason it frequently gets damaged, or external phenomena renders it useless.
TAS and TNG opened a can of worms in using molecular patterns to reconstitute a character or restore them to health. (The person doesn't remember anything that happened after they last beamed out.) Which leads to the thorny question why you can't beam up someone who just died in your landing party and restore them to life, as the "alive" pattern is still in the buffer?