Ah! I am dumb. I should've noticed that! I was fretting over nothing. Thank you very much. Final code, working!

import java.io.File;
import java.io.FileNotFoundException;
import java.util.Formatter;
import java.util.Scanner;

public class salaries
{
   public static void main( String[] args ) throws Exception
   {
      // open the text file for reading with a Scanner

      	String[] ssn = new String[100]; // stores Social Security Number
		double[] salaries = new double[100];
		int[] years = new int[100];
		int howmany = 0;
		
		howmany = InputData (ssn, salaries, years);
		Calculation(salaries, years, howmany);
		Output(ssn, salaries, years, howmany);
   }

		public static int InputData(String[] social, double[] sal, int[] years) throws FileNotFoundException
		{
		Scanner input = new Scanner( new File( "salaries.txt" ) );
		int i = 0;
		while ( input.hasNext())
		{	
		social[i] = input.next();
			
		sal[i] = input.nextDouble();	
		
		years[i]  = input.nextInt();
		
		i += 1;
		}	
	     input.close(); // close file
		return i;
		
		}
		public static void Calculation(double[] sal, int[] years, int howmany)
		{
		for(int i = 0; i < howmany; i++)	
		{
		if (years[i] >= 0 && years[i] <= 5)
			sal[i] *= 1.03;
		if (years[i] >= 6 && years[i] <= 10)
			sal[i] *=1.04;
		if (years[i] >= 11)
			sal[i] *=1.05;
		}
		}
		public static void Output(String[] social, double[] sal, int[] years, int howmany) throws FileNotFoundException
		{
			Formatter output = new Formatter("updated.txt");
			for (int i = 0; i < howmany; i++)
			{
			output.format("SSN: %s ", social[i]);
			output.format("New Salary: $%.2f \r\n", sal[i]);

			}
			output.close();
		}
}

I changed that with my teachers help and now get this error
Exception in thread "main" java.util.IllegalFormatConversionException: f != java.lang.String
at java.util.Formatter$FormatSpecifier.failConversion(Unknown Source)
at java.util.Formatter$FormatSpecifier.printFloat(Unknown Source)
at java.util.Formatter$FormatSpecifier.print(Unknown Source)
at java.util.Formatter.format(Unknown Source)
at java.util.Formatter.format(Unknown Source)
at salaries.Output(salaries.java:57)
at salaries.main(salaries.java:19)

Teacher told me to change a part:

import java.io.File;
import java.io.FileNotFoundException;
import java.util.Formatter;
import java.util.Scanner;

public class salaries
{
   public static void main( String[] args ) throws Exception
   {
      // open the text file for reading with a Scanner

      	String[] ssn = new String[100]; // stores Social Security Number
		double[] salaries = new double[100];
		int[] years = new int[100];
		int howmany = 0;
		
		howmany = InputData (ssn, salaries, years);
		Calculation(salaries, years, howmany);
		Output(ssn, salaries, years, howmany);
   }

		public static int InputData(String[] social, double[] sal, int[] years) throws FileNotFoundException
		{
		Scanner input = new Scanner( new File( "salaries.txt" ) );
		int i = 0;
		while ( input.hasNext())
		{	
		social[i] = input.next();
			
		sal[i] = input.nextDouble();	
		
		years[i]  = input.nextInt();
		
		i += 1;
		}	
	     input.close(); // close file
		return i;
		
		}
		public static void Calculation(double[] sal, int[] years, int howmany)
		{
		for(int i = 0; i < howmany; i++)	
		{
		if (years[i] >= 0 && years[i] <= 5)
			sal[i] *= 1.03;
		if (years[i] >= 6 && years[i] <= 10)
			sal[i] *=1.04;
		if (years[i] >= 11)
			sal[i] *=1.05;
		}
		}
		public static void Output(String[] social, double[] sal, int[] years, int howmany) throws FileNotFoundException
		{
			Formatter output = new Formatter("updated.txt");
			for (int i = 0; i < howmany; i++)
			{
			output.format("SSN is %f", social[i]);
			output.format("New Salary is %f", sal[i]);
			output.close();
			}
			
		}
}

still not working, new error message

Exception in thread "main" java.util.IllegalFormatConversionException: f != java.lang.String
	at java.util.Formatter$FormatSpecifier.failConversion(Unknown Source)
	at java.util.Formatter$FormatSpecifier.printFloat(Unknown Source)
	at java.util.Formatter$FormatSpecifier.print(Unknown Source)
	at java.util.Formatter.format(Unknown Source)
	at java.util.Formatter.format(Unknown Source)
	at salaries.Output(salaries.java:57)
	at salaries.main(salaries.java:19)

Current code:

import java.io.File;
import java.io.FileNotFoundException;
import java.util.Formatter;
import java.util.Scanner;

public class salaries
{
   public static void main( String[] args ) throws Exception
   {
      // open the text file for reading with a Scanner

      	String[] ssn = new String[100]; // stores ssn
		double[] salaries = new double[100];
		int[] years = new int[100];
		int howmany = 0;
		
		howmany = InputData (ssn, salaries, years);
		Calculation(salaries, years, howmany);
		Output(ssn, salaries, years, howmany);
   }

		public static int InputData(String[] social, double[] sal, int[] years) throws FileNotFoundException
		{
		Scanner input = new Scanner( new File( "salaries.txt" ) );
		int i = 0;
		while ( input.hasNext())
		{	
		social[i] = input.toString();
			
		sal[i] = (double)input.nextDouble();	
		
		years[i]  = input.nextInt();
		
		i += 1;
		}	
	     input.close(); // close file
		return i;
		
		}
		public static void Calculation(double[] sal, int[] years, int howmany)
		{
		for(int i = 0; i < howmany; i++)	
		{
		if (years[i] >= 0 && years[i] <= 5)
			sal[i] *= 1.03;
		if (years[i] >= 6 && years[i] <= 10)
			sal[i] *=1.04;
		if (years[i] >= 11)
			sal[i] *=1.05;
		}
		}
		public static void Output(String[] social, double[] sal, int[] years, int howmany) throws FileNotFoundException
		{
			Formatter output = new Formatter("updated.txt");
			for (int i = 0; i < howmany; i++)
			{
			output.format("SSN is %f", social[i]);
			output.format("New Salary is %f", sal[i]);
			output.close();
			}
			
		}
}

I am wondering what is going on this this. This input file is attached at the bottom too.

I really need help with this. fuzzy's idea still got me this. I am so confused about this
Exception in thread "main" java.util.InputMismatchException
at java.util.Scanner.throwFor(Unknown Source)
at java.util.Scanner.next(Unknown Source)
at java.util.Scanner.nextDouble(Unknown Source)
at salaries.InputData(salaries.java:30)
at salaries.main(salaries.java:17)