1. You may be seeing the highlight rectangle. Add -highlightthickness => 0, to your canvas.
(Is the highlightthickness the reason it looks like there is an extra pixel?)

2. the reason you are seeing red background is that createRectangle does not draw two edges.

        $canvas->createRectangle(x1, y1, x2, y2, ?option, value, optio
+n, value, ...?)

       The arguments x1, y1, x2, and y2 give the coordinates of two di
+agonally opposite corners of the
       rectangle (the rectangle will include its upper and left edges 
+but not its lower or right edges).
[download]

Does the following do what you want ?

#!/usr/bin/perl
use warnings;
use strict;
use Tk;
# uncomment if module is installed
# use Tk::WidgetDump;

my ($dx,$dy);
my $mw  = Tk::MainWindow->new();
# kcot gently confirmed that 100x100 in geometry means 
# from 0,0 to 100,100 aka 101 pixels!!
#$mw->geometry("99x99");

# main underlying canvas is filled with RED
my $can = $mw->Canvas(
                -height => 100,
                -width  => 100,
                -bg => 'red',
                -highlightthickness => 0,
)->pack( );

# used to dump coordinates
my %board;

# alternate colors for tales
my @alt_col = qw(gold2 green);

# squares for tales starting at 0,0
my ($sq_x,$sq_y) = (0,0);

foreach my $letter (('A'..'B')){
    unshift @alt_col, pop @alt_col;
    foreach my $num (1..2){
        # cycle colors
        unshift @alt_col, pop @alt_col;
        $can->createRectangle($sq_x, $sq_y, $sq_x+50,$sq_y+50,
            -fill => $alt_col[0],
            # outline undef means ransparent outline
      # if not specified defaults to black outline
      -outline => undef ,
            -tags=> ['first']
    );
        $board{$letter.$num} = {tx=>$sq_x,ty=>$sq_y,bx=>$sq_x+49,by=>$
+sq_y+49};
  # add 50
  $sq_x += 50;          
    }
    # reset x to 0 for new row
    $sq_x = 0;
    # add 50 to y
    $sq_y += 50;
    print "\n";
}

# legenda
print "ty = top Y tx = top X  by = bottom Y bx = bottom X\n";

# dump board coordinates
foreach my $key (sort keys %board){
    print   "$key -> ",
      ( map{"$_ $board{$key}{$_} "} 
        reverse sort keys %{$board{$key}}
      ),"\n";
}

$can->bind('first', '<1>', sub {&show_click();});
# uncomment if module is installed
# $mw->WidgetDump;
MainLoop;

sub show_click{
    my $ev = $can->XEvent;
    ($dx, $dy) = ($ev->x, $ev->y);
    print "CLICKED  $dx  $dy\n";
    my $cur_id = ($can->find('withtag','current'))[0];
    print "current canvas $cur_id\n\n";    
}
[download]

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