I didn’t see this in the Elixir deploy that I did just a few hours ago, so it might be a problem specific to the local environment.
Maybe try examining the image’s ultimate filesystem directly:
fly console --user root
(This doesn’t require a preexisting Machine, in contrast to fly ssh console.)
Then…
cd /app
ls -ld / . bin bin/migrate
head -1 bin/migrate | od -c # double-check
That last one gives a character-by-character view of the first line of the file—including the exact ending sequence.