Why it probably happened:
Docker Compose tracks containers by project name + service name, not by container_name. Running docker compose up in different folders with the same service name but different container_name causes Compose to stop containers from the other project because it thinks they belong to the same service.

How to fix:

Use different service names in each compose file,

Or use the same service names but run with different project names via docker compose -p <project_name> up -d

Though, tell me if it's not the case.