As George_Sherston mentioned above, the parentheses put a banana into $1. Here is just another way to circumvent that:

$var = quotemeta('apple (banana) cherry');
$line = 'apple (banana) cherry kiwi lemon melon';
$line =~ s/$var//;
[download]

That would be equal to:

$var = 'apple \\(banana\\) cherry';
$line = 'apple (banana) cherry kiwi lemon melon';
$line =~ s/$var//;
[download]

Thus perl wouldn't catch the banana, because the parentheses were escaped.

-- 
arneb@emergency:~ > perl -MO=Deparse -e "(0); #Confusing perl..." 2> /dev/null
'???';
arneb@emergency:~ >