Honestly, Star Trek isn’t good enough scifi for me to think too hard about this problem. None of the writers seem to really think about the large implications of transporter and replicator tech. You may get an episode about using the transporter buffers to smuggle refugees, but then the concept wont come back up.

Better examples of world building with replicator tech would be Diamond Age or the Bobiverse books. Both have thought out limitations that prevent casual replication of living animals.