I have a fan theory to explain this contradiction.
Yes, something like that. My head canon on this stuff: However it also ties into the replicator. Replicators can't create living creatures because too much of being 'living' is tied up in all those quantum states. It seems to indicate that it is not possible to write such a pattern or normally copy it. Instead, when the transporter begins the process, it puts the item being transported into the 'transporter buffer' that saves the pattern and all that quantum information. This is apparently a destructive process and not normally copiable. This buffered information is then used to reform the new body. It's how Scotty survived for years in the dyson sphere in a TNG episode, by storing himself in the buffer, although others did not survive the process. The inability of copying the buffer pattern is something like putting Schrodinger's cat in a box, and them just dumping it out again in the same state. It's not possible to look in the box to copy that information because trying messes with all that location and momentum uncertainty.
However, we have various episodes where it was copied. Kirk in TOS during a cosmic storm, where we get a good and evil Kirk, and then something in TNG with Riker. this is why I said it is not normally copyable. There are apparently cases where the pattern can be split, copied, or otherwise modified. I don't even want to think about episodes where the transporter became a fountain of youth machine and made everybody teenagers again physically, but they kept all their memories. I mean, that, like the Genesis bomb, is pretty much a setting changing tech that by all accounts should have repeatable and if nothing else used for medical issues.