I ran your program which output:

Not ok cases

N65, N25
N65, N25
too many lats or lons
Err: 1

65P, E25
65P, E25
too many lats or lons
Err: 1

91, 47
91, 47
numbers are too big
LAT: 91 LON: 47

65P, W25
65P, W25
mixed languages
Err: 1

100 E, 91 N
N91 ,E100 
numbers are too big
LAT: 91 LON: 100

47.9805, -186.5586
47.9805, -186.5586
numbers are too big
LAT: 47.9805 LON: -186.5586
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You have 13 error tests in your program:

1:   74         if(($ENG >0) && ($FIN > 0)) {
     75                 print "mixed languages\n";
     76                 $err++
     77         }
2:   78         elsif (($FIN>0) && ( ($H{I}+$H{L})>1 || ($H{E}+$H{P})>
+1 )) {
     79                 print "too many lats or lons\n";
     80                 $err++
     81         }
3:   82         elsif (($ENG>0) && ( ($H{N}+$H{S})>1 || ($H{W}+$H{E})>
+1 )) {
     83                 print "too many lats or lons\n";
     84                 $err++
     85         }
4:   86         elsif ($H{E}>1) {
     87                 print "too many E\n";
     88                 $err++
     89         }
5:   90         elsif ($H{I}>1) {
     91                 print "too many I\n";
     92                 $err++
     93         }
6:   94         elsif ($H{L}>1) {
     95                 print "too many L\n";
     96                 $err++
     97         }
7:   98         elsif ($H{P}>1) {
     99                 print "too many P\n";
    100                 $err++
    101         }
8:  102         elsif ($H{W}>1) {
    103                 print "too many W\n";
    104                 $err++
    105         }
9:  106         elsif ($H{S}>1) {
    107                 print "too many S\n";
    108                 $err++
    109         }
10: 110         elsif ($H{N}>1) {
    111                 print "too many N\n";
    112                 $err++
    113         }
...
11: 133         elsif ($comma_count > 3) {
    134                 print "too many commas\n";
    135                 $err++
    136         }
12: 137         elsif ($dot_count > 2) {
    138                 print "too many dots\n";
    139                 $err++;
    140         }
...
13: 169                 if ($coords =~ /^[-+]?([1-8]?\d(\.\d+)?|90(\.0
++)?),\s*[-+]?(180(\.0+)?|((1[0-7]\d)|([1-9]?\d))(\.\d+)?    169 )$/) 
+{
    170                         print "all ok\n";
    171                 } else {
    172                         print "too big numbers\n";
    173                 }
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But only 1, 2, 3 and 13 are actually tested for in your test data.

Also, tests 4 through 10 can be combined into one test:

        elsif ( my @keys = grep $H{ $_ } > 1, keys %H ) {
                for ( @keys ) {
                        print "too many $_\n";
                        $err++
                }
        }
[download]

Although this test will never execute because tests 2 and 3 take presedense.

Also this:

     30         my %H;
...
     61         $H{E} = ($_ =~ tr/E//);
     62 
     63         $H{I} = ($_ =~ tr/I//);
     64         $H{P} = ($_ =~ tr/P//);
     65         $H{L} = ($_ =~ tr/L//);
     66 
     67         $H{W} = ($_ =~ tr/W//);
     68         $H{N} = ($_ =~ tr/N//);
     69         $H{S} = ($_ =~ tr/S//);
[download]

Could be simplified a bit:

        my %H = (
                E => tr/E//,

                I => tr/I//,
                P => tr/P//,
                L => tr/L//,

                W => tr/W//,
                N => tr/N//,
                S => tr/S//,
                );
[download]

And finally, you use tr/// for counting but you could also use it in a few other places:

      7         $in =~ s/[NWSEIPL]//g;

        $in =~ tr/NWSEIPL//d;

     39         s/[^0-9NWSEIPL,.+-]/ /g;

        tr/0-9NWSEIPL,.+-/ /c;

    122                 s/ /./g;

                tr/ /./;

    126                 s/,/./g;

                tr/,/./;

    148                 s/[NE]//g;

                tr/NE//d;

    156                 s/[IP]//g;

                tr/IP//d;
[download]