The  ^ regex metacharacter at the very beginning of a character set or class complements the characters defined for the set.

The character class regex  [^\s-~] matches any character that is not a whitespace character, a literal '-' (dash or hyphen) or a literal '~' (tilde). A 'Y' is not any of those characters, so it matches.

BTW — the character set  [^\s-~] is better written as  [^-\s~] so that the '-' character is not misunderstood (by the programmer or maintainer, not by Perl) as a character set range metacharacter. I'm guessing you are not running with warnings (and strictures), otherwise Perl would have complained about this:

>perl -wMstrict -le "my $rx = qr{ [^\s-~] }xms;  print $rx;"
False [] range "\s-" in regex; marked by <-- HERE 
in m/ [^\s- <-- HERE ~] / at -e line 1.
(?msx-i: [^\s-~] )
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