here...
I used myCountForGrow and make some changes to the leaves...

maybe your code is clearer when you use pushMatrix and popMatrix.
The you can isolate the different scale and translate from each other
(instead of scaling it back again with -value).

I also made a few lines (in draw() ) to show the circles but
they don't make much sense. At the moment they are commented out.

Greetings, Chrisir  

1. Stem myStem;
2. Circle circles[];
3. Flower flowers = new Flower();
4. float scaleFactor=0.5;
5. int myCountForGrow=0;
6. void setup() {
7.   size(floor(400*scaleFactor), floor(800*scaleFactor));
8.   myStem = new Stem(200, 800);
9.   flowers = new Flower (0, 0);
10.   //moved this to setup, no need to recreate each frame
11.   circles = new Circle[6];
12.   circles[0]  = new Circle(0, -40, 50, 50);
13.   circles[1]  = new Circle(0, -40, 50, 50);
14.   circles[2]  = new Circle(0, -40, 50, 50);
15.   circles[3]  = new Circle(0, -40, 50, 50);
16.   circles[4]  = new Circle(0, -40, 50, 50);
17.   circles[5]  = new Circle(0, 0, 50, 50);
18.   // also smooth only needs to be called once
19.   // unless ther is a noSmooth() somewhere
20.   smooth();
21. }
22. void draw() {
23.   float grow = 0;
24.   //translate(myStem.initalloX, myStem.initalloY); 
25.   myStem.drawStem();
26.   // set centre point
27.   // translate(myStem.initalloX, ((frameCount>250)?myStem.initalloY-      500:myStem.initalloY-(2*myCountForGrow)));
28.   translate(myStem.initalloX, myStem.initalloY-(myCountForGrow));
29.   if (frameCount>10) {
30.     flowers.grow();
31.     flowers.display();
32.   }
33.   // show the circles
34.   //for (int i = 0 ; i < circles.length; i++)
35.   //  circles[i].display();
36.   // 
37.   if (myCountForGrow<200)
38.     myCountForGrow+=1.28;
39. }
40. class Stem {
41.   int initalloX=200;
42.   int initalloY=800;
43.   Stem(int tempInitalloX, int tempInitalloY) {
44.     initalloX = tempInitalloX;
45.     initalloY = tempInitalloY;
46.   }
47.   void drawStem() {
48.     background(#0DBADB);
49.     scale(scaleFactor, scaleFactor);
50.     stroke (12, 149, 11);
51.     fill (12, 149, 11);
52.     strokeWeight(10);
53.     //line(initalloX, initalloY, initalloX, ((myCountForGrow>250)?initalloY-500:initalloY-(2*myCountForGrow)));
54.     /*
55.     if (myCountForGrow>250)
56.      line(initalloX, initalloY, initalloX, (initalloY-500));
57.      else
58.      line(initalloX, initalloY, initalloX, (initalloY-(2*myCountForGrow)));
59.      */
60.     line(initalloX, initalloY, initalloX, (initalloY-(myCountForGrow)));
61.     //stem1
62.     if (myCountForGrow>101) {
63.       noStroke();
64.       translate(initalloX, initalloY-myCountForGrow*.53);
65.       scale(min((float)(myCountForGrow-100)/100, 1), min((float)(myCountForGrow-100)/100, 1));
66.       beginShape();
67.       vertex(0, 0);
68.       // leaf left
69.       bezierVertex(-40, -5, -30, -40, -80, -20);
70.       bezierVertex(-47, -16, -52, 8, 0, 0);
71.       endShape(CLOSE);
72.       scale(1/min((float)(myCountForGrow-100)/100, 1), 1/min((float)(myCountForGrow-100)/100, 1));
73.       translate(-initalloX, -(initalloY-myCountForGrow*.53));
74.       noStroke();
75.     }
76.     //stem2
77.     if (myCountForGrow>151) {
78.       //  noStroke();
79.       translate(initalloX, initalloY-myCountForGrow*.26-30);
80.       scale(-min((float)(myCountForGrow-110)/150, 1), min((float)(myCountForGrow-110)/150, 1));
81.       beginShape();
82.       vertex(0, 0);
83.       // leaf right
84.       bezierVertex(-40, -5, -30, -40, -80, -20);
85.       bezierVertex(-47, -16, -52, 8, 0, 0);
86.       endShape(CLOSE);
87.       scale(-1/min((float)(myCountForGrow-110)/150, 1), 1/min((float)(myCountForGrow-110)/150, 1));
88.       translate(-initalloX, -(initalloY-myCountForGrow*.26-30));
89.     }
90.   }
91. }
92. class Circle {
93.   int c1 = 0;
94.   int c2 = -40;
95.   float c3 = 50;
96.   float c4 = 50;
97.   Circle(int tc1, int tc2, float tc3, float tc4) {
98.     c1 = tc1;
99.     c2 = tc2;
100.     c3 = tc3;
101.     c4 = tc4;
102.   }
103.   void display()
104.   {
105.     ellipse(c1, c2, c3, c4);
106.   }
107. }
108. class Flower {
109.   float centerX;
110.   float centerY;
111.   float posX;
112.   float posY;
113.   float maxSize = 51;
114.   float maxFactor = 40;
115.   float sizes = 0;
116.   float factor = 0;
117.   float speed = 0.17;
118.   Flower() {
119.   }
120.   Flower(float _centerX, float _centerY)
121.   {
122.     centerX = _centerX;
123.     centerY = _centerY;
124.   }
125.   void setCenter(float x, float y)
126.   {
127.     centerX = x;
128.     centerY = y;
129.   }
130.   void display()
131.   {
132.     for (int i = -18; i < 360; i+=72)
133.     {
134.       posX = centerX + cos(radians(i)) * factor;
135.       posY = centerY + sin(radians(i)) * factor;
136.       noStroke();
137.       fill(170, 14, 24); // blue
138.       ellipse(posX, posY, sizes, sizes);
139.     }
140.     fill(14, 17, 170);
141.     ellipse(centerX, centerY, sizes, sizes );
142.   }
143.   void grow()
144.   {
145.     factor = (factor < maxFactor )?  factor + speed: maxFactor;
146.     sizes = (sizes < maxSize )?  sizes + speed*1.3 : maxSize;
147.   }
148. }// end of Flower