it took way to long to find the answer to this (around 20 hours!), but I finally got it to work by doing a rewrite before reverse proxy. note that this only works for single subdirs. see the subfolder problem
my config now:
site-one.com {
encode gzip
import headers
rewrite * /site-one{uri}
reverse_proxy localhost:8080
log {
output file /var/log/caddy/site-one.log
}
}