We just solved a problem on IRC where a new site was not indexing, because the records were UNIMARC and the site was MARC21, because /etc/koha/koha-sites.conf had not been edited priori to running koha-create.
To avoid situations like this, we could display the config values (from /etc/koha/koha-sites.conf or another file specified with the --configfile option) that are about to be used and ask the user "does this look ok?".
The configfile could have a setting to disable the question for those who are confident to avoid it.
This happens quite often - mismatch of MARC flavours