Fixing the || bug, refactoring the expression and commenting gives this:

use strict;
use warnings;

my $A = -4;
my $w = 500;

my $re = qr
  /
  ^\s*        #Start of line followed by any amount of white space
    \Q$A\E    #Litteral contents of $A
    \s*       #Any amount of white space
    \*?       #Optional *
    \s*cos    #Any amount of white space followed by cos
      \s*       #Any amount of white space
    (       #Start a capture group
      \s        #At least one white space character
      \Q$w\E    #Litteral contents of $w
      \s*t      #Any amount of white space followed by t
    |       #Match either expression (i.e. - with or without brackets)
      \(\s*     #( followed by any amount of white space
      \Q$w\E    #Litteral contents of $w
      \s*t      #Any amount of white space followed by t
      \s*\)     #Any amount of white space followed by )
    )       #End of capture group
    \s+A      #At least one white space character followed by A
  \s*$
  /x;

while (<DATA>)
  {
  print "Match: $_" if $_ =~ $re;
  }
  
__DATA__
-4cos 500t A
-4 cos 500t A
-4*cos 500t A
-4*cos(500t) A
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