As moritz said, your @array appears to be global, so it's not getting recreated each time through your loop, and all your hash keys are getting assigned a reference to the same array. Here's how I'd rewrite your loop to eliminate that array and clarify some things:

my $j = 0; # file/column number
foreach $file (@files){
    open(INP,"$file") or die "Cannot open file :$!\n";
    while (<INP>){
        chomp;
        my($key,$value) = split "\t";
        if(exists $trans{$key}){
            $trans{$key}[$j] = $value;
        }
    }
    close(INP);
    $j++;
}
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When you split a line into an array and then start accessing the elements directly like $line[0], that's a good sign you might want to split it into named scalars like $key and $value instead, so you don't have to remember later what array index held what. I think it also makes it easier to see what I'm doing there when I assign the $value to the $j-th element of the array pointed to by the $key of the hash.