Turn the list of folders into a single regex, then do your test. Add boundary conditions to the regex as required.

#!/usr/bin/perl -w 
use strict;  
use warnings;

my @folders = qw(inc Inc iNc incr src Src);
my $folders_re = join '|', map {quotemeta} @folders;

my $mk = "./media/common/max/tail/common.mk:    $(PROJECT_ROOT)/../../
+Utils/inC";

my @folder_match;

if ($mk !~ /$folders_re/i) {
    push @folder_match ,$mk;
}

print "@folder_match\n";
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