You didn't show how you set $_. The following works as expected for me. It only prints the apple line:

use strict;
use warnings;

my $fruit = "apple";
while (<DATA>) {
    if ( $_ =~ /$fruit/) {
        print "$_";
    }
}

__DATA__
 TEXAS,apple,2,E,0,0000, 0030,     0145,      0030,  0145,   0100,    
+ 0030,  0145,     0000,   0000,      3
 NEVADA,GRAPE,2,E,0,0000, 0030,     0145,      0030,  0145,   0100,   
+  0030,  0145,     0000,   0000,      3
 MONTANA,PEAR,2,E,0,0000, 0030,     0145,      0030,  0145,   0100,   
+  0030,  0145,     0000,   0000,      3
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