How do you deploy? I usually run a script that changes the permissions and user after upload if I upload with SFTP:
#!/bin/sh
DIRS="assets content kirby site thumbs"
FILES="index.php"
for dir in $DIRS;do
sudo chown -R www-data.www-data "$dir"
find "$dir" -type d -print0 | xargs -0r sudo chmod 775
find "$dir" -type f -print0 | xargs -0r sudo chmod 664
find "$dir" -type f \( -name *.pl -o -name *.cgi \) -print0 | xargs -0r sudo chmod 775
done
for file in $FILES;do
sudo chown www-data.www-data "$file"
sudo chmod 664 "$file"
done
exit 0;