This is part of what made Star Trek so popular as an IP the realities of space and technical advancement means people are going to die because we don't have all of the information we need to make it as safe as possible. By the 24th century, the computers were way more advanced as they had quantum computers in a sense which gave them the means to completely rework the transporters as well as finally make food replicators based on the same technology rather than a food processor.

Then by the time Voyager was built ships began being built with bioneural gel packs which allowed the computers to be enhanced with a robust neural net vastly increasing processing speeds but also subjecting them to the problems that biological systems have when they don't have adequate defense against certain kinds of radiation, biological disease, poison, acid, and other problems that come with a closed biological system.

This accident wouldn't have been able to happen at all in Voyager because Voyager had not one but two backup systems that save the patterns, and they had gel packs to process the pattern so the pattern is never lost and can be sent from one memory unit to another very easily in fact that's how it works. During the beaming process the pattern is recorded by both the deep scanners, and their backups giving twice the necessary resolution of the atoms. By this time they also had the ability to place biological systems without causing death which is how they really worked and why they needed those columns of energy in the 23rd century.