While I readily agree that autogenerated config files should not have this problem, and that YAML works that way, especially in the trial phase, this can confuse users. Warning or, preferably, erroring out would be appreciated.

If you run with a configuration like:

scrape_configs:
  - job_name: 'prometheus_system'
    target_groups:
    - targets: ['localhost:9100']

scrape_configs:
  - job_name: 'foo_system'
    target_groups:
    - targets: ['foot:9100']

the former scrape_configs is silently discarded. While that's the obvious case, constructs like

scrape_configs:
  - job_name: 'prometheus_system'
    target_groups:
    - targets: ['localhost:9100']

rule_files:
  - 'prometheus.rules'

scrape_configs:
  - job_name: 'foo_system'
    target_groups:
    - targets: ['foo:9100']

are silently discarded as well.

So to summarize: Yes, I fat-fingered, but principle of least surprise would be to error out instead of silently carrying on.