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Here is what my reworked code looks like. I neatened it up as much as I could. Changed some of the semantics of it. I also tried to add some faster exit points and checks to prevent errors.

Any further critiques?

 /**
 * @author :KyleMHB
 * Project Number :0002
 * Project Name :Anagramatic
 * IDE :NETBEANS
 * Goal of Project - 
 * Capture user input, compare to a dictionary file for anagrams,
 * output number of matches and the matches.
 */
package anagramatic;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
import java.util.List;
import java.util.Scanner;
import javax.swing.JOptionPane; 

public class Anagramatic {
public static void main(String[] args) throws FileNotFoundException{
 String anagram=getInput("Enter the word you would like to process");
 List<String> words=readAnagramsFromFile(anagram, new File("words.txt"));
 String output= formatOutput(anagram,words);
 displayOutput(output);
}//pvsm

private static String getInput(String prompt) {
 String input = JOptionPane.showInputDialog(null,prompt);
 return input;
}//getInput

 private static List readAnagramsFromFile(String word, File f) 
 throws FileNotFoundException{
 ArrayList<String> anagrams = new ArrayList<>(); 
 try(Scanner s = new Scanner(f)){
 while(s.hasNext()){
 String candidate=s.next();
 if ( (candidate.length()==word.length()) &&
 (checkMatch(word,candidate)==true)){
 anagrams.add(candidate);
 }
 }
}
 return anagrams;
}//readFile

private static boolean checkMatch(String word, String candidate) {
 char[] wordArray = word.toCharArray();
 char[] candidateArray = candidate.toCharArray();
 if (Arrays.equals(wordArray, candidateArray)){
 return false;
 }
 Arrays.sort(wordArray);
 Arrays.sort(candidateArray);
 if(Arrays.equals(wordArray, candidateArray)){
 return true;
 }
 /**I did not use an else function for the the below return
 *because if (Arrays.equals(wordArray, candidateArray))==true
 *it will break on the return*/
 return false;
 
}//match

private static String formatOutput(String original, List<String> words) {
 StringBuilder output=new StringBuilder("[ ");
 int counter=0;
 Iterator<String> wordIt =words.iterator();
 while(wordIt.hasNext()){
 output.append(wordIt.next());
 if(wordIt.hasNext()){
 output.append((++counter % 8 == 0)? ",\n" : ", ");
 }
 }
 output.append(" ]");
 return ("The Anagram "+original+" has "+words.size()+" matches.\n\nThey are:\n"+output.toString());
}//formatOutput
 

private static void displayOutput(String output){
 JOptionPane.showMessageDialog(null,output);
}//displayOutput
}