That's causing your problem. You are only using the chunk before the first space for each file.

I haven't had a chance to test this in your exact usage situation, but try the following. It replaces spaces in the file names with escaped spaces.

#!/usr/bin/perl
@files = glob("*.msg");
foreach $file(@files) {
    $file =~ s/ /\\\ /g;
    $cmd = "perl script.pl < $file";
    system($cmd);
}
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