If the problem was that you were not catching those 57's, it was because of those blanks within [], so just modify your regexp to allow it:

use strict;
use warnings;

while (my $file_content = <DATA>) {
    if ( $file_content =~ m/Vc3/ ) {
        my @numbers = $file_content =~ /\[\s*(\d+)\s*\]/g;#modified

        { local $,=':'; print @numbers; print $/ }
    }
}

__DATA__
            Item no.0:  NameDepth [2]

        <0>   Class: [1] NetElementObjectClass                Instance
+: (int) [2]
        <1>   Class: [ 57 ] Vc3TtpSnkObjectClass                Instan
+ce: (int) [3]
                Item no.1:  NameDepth [2]

        <0>   Class: [1] NetElementObjectClass                Instance
+: (int) [2]
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This prints:

57:3
57
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