$text =~ s/^\xef\xbb\xbf//g does remove the offending bytes if your string contains the characters you described. (Well, it'll delete the leading sequence, and removing the ^ will have it delete the others too.)
Since you repeatedly claim it doesn't, your data is different than you describe, and we can't help you until you provide a better description of your data (e.g. the output of sprintf "%vX", $string).
fyi, EF BB BF is the UTF-8 encoding of U+FEFF, which is the Byte Order Mark if at the start of the file, and the Zero Width No-Break Space elsewhere.
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