If the warning is meaningless as others have stated, you can catch all warnings by specifying a $SIG{__WARN__} handler, and prevent printing of that specific one:

use warnings;
use strict;

$SIG{__WARN__} = sub {
    my $warn = shift;
    if ($warn !~ /^A thread exited/){
        print $warn;
    }
};

warn "blah blah warning\n";
warn "A thread exited...\n";
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Output:

blah blah warning
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update: I just realized that the signal handler for warn does not appear to be re-entrant for a warn call from within the handler itself... that is, you can replace my print statement inside the handler with warn, and re-throw the actual warning:

perl -E '$SIG{__WARN__}=sub{say "handler";warn $_[0] if $_[0]!~/^A thr
+ead/}; warn "blah"; warn "A thread";'
handler
blah at -e line 1.
handler
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/update