Leaving aside the efficiency of using MD5 for this purpose (see the discussion here and in the marked duplicate of that question), basically the answer is that what you have is what a uniform distribution really looks like.
That might seem counter-intuitive, but it's easily demonstrable either mathematically or by experiment.
As a kind of motivating example, consider the task of choosing exactly 64 numbers in the range 0-63. The odds that you will get one per bucket are very close to 0. There are 6464 possible sequences, of which 64! contain all 64 numbers. The odds of getting one of these sequence is about one in 3.1×1026. In fact, the odds of getting a sequence in which no element appears three times is less than one in a thousand (it's about .000658). So it's almost certain that a random uniform sample of 64 numbers in the range 0-63 will have some triplets, and it's pretty likely that there will be some quadruplet. If the sample is 100 numbers, those probabilities just get even bigger.
But the maths are not so easy to compute in general, so here I chose to illustrate by experiment :-), using random.org, which is a pretty reliable source of random numbers. I asked it for 100 numbers in the range 0-63, and counted them (using bash, so my "graph" is not as pretty as yours). Here are two runs:
First run:
Random numbers:
44 17 50 11 16 4 24 29 12 36
27 32 12 63 4 30 19 60 28 39
22 40 19 16 23 2 46 31 52 41
13 2 42 17 29 39 43 9 20 50
45 40 38 33 17 45 28 6 48 12
56 26 34 33 35 40 28 44 22 10
50 55 49 43 63 62 22 50 15 52
48 54 53 26 4 53 13 56 42 60
49 30 14 55 29 62 15 13 35 40
22 38 37 36 10 36 5 41 43 53
Counts:
X X X
X XX X X XX X X X X X
X X X XX XXX X X X XXX X XX XXXXXXXX XXX XX XX X XX
X XXX XXXXXXXXX XX XXX XXXXXXXXXXXXXXXXXXXXX XXX XXXXX X XX
----------------------------------------------------------------
1 1 1 1 1 2 2 2 2 2 3 3 3 3 3 4 4 4 4 4 5 5 5 5 5 6 6
0 2 4 6 8 0 2 4 6 8 0 2 4 6 8 0 2 4 6 8 0 2 4 6 8 0 2 4 6 8 0 2
Second run:
Random numbers:
41 31 16 40 1 51 17 41 27 46
24 14 21 33 25 43 4 36 1 14
40 22 11 22 30 19 23 63 39 61
8 55 40 6 21 13 55 13 3 52
17 52 53 53 7 21 47 13 45 57
25 27 30 48 38 55 55 22 61 11
11 28 45 63 43 0 41 51 15 2
33 2 46 14 35 41 5 2 11 37
28 56 15 7 18 12 57 36 59 51
42 5 46 32 10 8 0 46 12 9
Counts:
X X X X
X X XX XX XX X X X
XXX X XX XXXXX X XX X XX X X X XX X XX XXX X X X X
XXXXXXXXXXXXXXXXXXXX XXXXX XX XXXX XXXXXXXXX XXXX XXX XXX X X X
----------------------------------------------------------------
1 1 1 1 1 2 2 2 2 2 3 3 3 3 3 4 4 4 4 4 5 5 5 5 5 6 6
0 2 4 6 8 0 2 4 6 8 0 2 4 6 8 0 2 4 6 8 0 2 4 6 8 0 2 4 6 8 0 2
You could try this with your favourite random number generator, playing around with the size of the distribution. You'll get the same sort of shape.