Well, I can't reproduce it locally. What happens if you edit wakaba.pl and change

spam_engine(
	query=>$query,
	trap_fields=>SPAM_TRAP?["name","link"]:[],
	spam_files=>[SPAM_FILES],
	charset=>CHARSET,
) unless $whitelisted;

to

spam_engine(
	query=>$query,
	trap_fields=>SPAM_TRAP?["name","link"]:[],
	spam_files=>[SPAM_FILES],
	charset=>CHARSET,
	excluded_files=>["file"],
) unless $whitelisted;