Same issue here — status is stuck on “stop” for us as well. I ended up ssh’ing into the container and killing the process to prevent the stopping instance from serving any traffic, but fly status --all still lists the instance (it’s been in “stopping” state for >1h; the culprit is the last row, ID b1f23696):
Instances
ID PROCESS VERSION REGION DESIRED STATUS HEALTH CHECKS RESTARTS CREATED
c8bed9ba app 46 ⇡ fra run running 1 total, 1 passing 0 35m58s ago
a460c025 app 44 fra stop complete 1 total, 1 passing 0 1h44m ago
702fe83e app 44 fra stop pending 0 2h0m ago
618bc21c app 42 fra stop complete 1 total, 1 passing 0 2h8m ago
b1f23696 app 41 fra stop running 1 total, 1 critical 0 2022-08-29T00:45:01Z