That rack tho ;)

Rack.java

/**
 * Created by Connor on 12/8/15.
 */
public class Rack {
    private Vial[][] rack;

    public Rack(){
        rack = new Vial[3][8]; //instantiates the rack when object is created
    }

    public Vial[][] getRack(){  //for the consolidate method
        return rack;
    }

    @Override //compile-time flag to catch little mistakes like tostring() instead of toString()
    public String toString() {//my toString() is messy af
        String str = "";
        boolean added = false;
        for (int i = 0; i < rack.length; i++) {
            for (int j = 0; j < rack[0].length; j++) {
                if (rack[i][j] != null){
                    if (added) str += "\n";//this just adds a new line after each time there is another vial to print
                    str += "Row "+i+" Col "+j+"\n"+ rack[i][j].toString()+"\n";
                    added = true;
                }
            }
        }
        if (str.length() == 0) return "";
        return str.substring(0,str.length()-1);//removes the ""\n" at the end so there isnt another newline at the end of the output
    }
    
    // Add a vial to the first empty position in the rack.
    // Return true if successful, false otherwise.
    public boolean add(Vial vial){
        for (int i = 0; i < rack.length; i++) {
            for (int j = 0; j < rack[0].length; j++) {
                if (rack[i][j] == null){
                    rack[i][j] = vial;
                    return true;
                }
            }
        }
        return false;
    }

    // Add a vial to the indicated position in the rack if it is empty.
    // Return true if successful, false otherwise.
    public boolean add(Vial vial, int row, int col){
        if (rack[row][col] == null){
            rack[row][col] = vial;
            return true;
        }
        else return false;
    }

    //Calculate the number of vials in the rack
    public int count(){
        int sum = 0;
        for (int i = 0; i < rack.length; i++) {
            for (int j = 0; j < rack[0].length; j++) {
                if (rack[i][j] != null)
                    sum++;
            }
        }
        return sum;
    }

    // Get the total quantity of a particular potion in all of
    // the vials the rack
    public double getQuantity(String potionName){
        int sum = 0;
        for (int i = 0; i < rack.length; i++) {
            for (int j = 0; j < rack[0].length; j++) {
                if(rack[i][j] != null){
                    sum += rack[i][j].getQuantity(potionName);
                }
            }
        }
        return sum;
    }

    // Get the quantity (weight in grams) of the entire rack
    public double getQuantity(){
        int sum = 0;
        for (int i = 0; i < rack.length; i++) {
            for (int j = 0; j < rack[0].length; j++) {
                if (rack[i][j] != null)
                    sum += rack[i][j].getQuantity();
            }
        }
        return sum;
    }

    // remove and return the vial at the specified location
    // return null if no vial was found
    public Vial remove(int row, int col){
        if (rack[row][col] != null){
            Vial temp = rack[row][col];
            rack[row][col] = null;
            return temp;
        }
        else return null;
    }

    // shift all the vials towards spot 0,0 in the array.  Do
    // not allow any open spots between vials.  Returns nothing.
    // Try and do this without creating a new array.
    public void consolidate() {
        Rack foo = new Rack(); //so much easier than not creating a new array... and its just as efficient (if not more)

        for (int i = 0; i < rack.length; i++) {
            for (int j = 0; j < rack[0].length; j++) {
                if (rack[i][j] != null) foo.add(rack[i][j]);
            }
        }
        this.rack = foo.getRack(); //points this.rack to foo's rack 
    }

    public void printVisual(){ //for fun
        for (int i = 0; i < rack.length; i++) {
            for (int j = 0; j < rack[0].length; j++) {
                if (rack[i][j] == null){
                    System.out.print("[ ]");
                }
                else System.out.print("[*]");
            }
            System.out.println();
        }
    }

    public static void main(String[] args) { //just to visualize the consolidate method
        Rack rack1 = new Rack();
        int col;
        int row;

        for (int i = (int) (Math.random()*20); i < 24; i++) {
            col = (int) (Math.random()*8);
            row = (int) (Math.random()*3);
            rack1.add(new Vial(),row,col);
        }//creates a completely random rack every time ran 

        rack1.printVisual();
        System.out.println("consolidated:");
        rack1.consolidate();
        rack1.printVisual();
    }
}

Vial.java

import java.util.ArrayList;
class Vial {
    private ArrayList<Potion> vial;
    public final double EPSILON =1E-14;

    public Vial(){
        vial = new ArrayList<Potion>(); //instantiates the vial ArrayList when object is created
    }

    @Override //compile-time flag to catch little mistakes like tostring() instead of toString()
    public String toString() { //another messy af toString() 
        String output = "";
        if (vial.size() == 0 || vial == null) return "";
        for (int i = 0; i < vial.size() - 1; i++) {//adds everything with a newline except the last 
            output += vial.get(i).toString() + "\n";
        }
        output += vial.get(vial.size()-1).toString(); //so that there isn't a newline at the end of the output

        return output;
    }

    public ArrayList<Potion> getVial(){
        return vial;
    }

    public double getQuantity() {
        double sum = 0;
        for (int i = 0; i < vial.size(); i++) {
            sum += vial.get(i).getQuantity();
        }
        return sum;
    }

    public double getQuantity(String name) {
        double sum = 0;
        for (int i = 0; i < vial.size(); i++) {
            if (vial.get(i).getDescription().equals(name)){
                sum += vial.get(i).getQuantity();
            }
        }
        return sum;
    }

    public boolean addPotion(Potion foo) {
        if (this.getQuantity() + foo.getQuantity() - 100 < EPSILON) {
            for (int i = 0; i < vial.size(); i++) {
                if (vial.get(i).getDescription().equals(foo.getDescription())){
                    vial.get(i).add(foo.getQuantity());
                    return true;
                }
            }
            vial.add(foo);
            return true;
        } else return false;
    }
}