You are probably talking about the unpredictability in the micro world as dictated by quantum mechanics (?) If this is how you mean it, it is an interesting question, and here are some thoughts about it.
Being unpredictable is not necessarily equivalent to being imperfect. On the contrary, unpredictability is the source of all beauty we witness in nature. By being unpredictable, through quantum mechanics, nature achieves the creation and manufacturing of perfect structures. It is not hard to see this if you look at the right places, a couple of which are briefly discussed below:
(i) The crystalline structure of matter. Perfect crystal symmetry, from the simplest to the most complex symmetry groups (from mathematics point of view,) lead to the perfect crystal structures we admire in nature. The laws of quantum mechanics that conspire for the organisation of matter in such perfect ways are totally probabilistic, and yet, the outcome is awesome.
(ii) The beautiful interference coloured patterns we observe on a thin film of oil floating on the water, or on the feathers of a peacock, is the result of the probabilistic properties of light in the form of photons.
Are two electrons or photons different? To answer this question you need to examine the way electrons or photons respond to various conditions we put them through. If for example we shoot two electrons perpendicularly into a uniform magnetic field, both at speed v, they will both follow circular paths of the same radius and they will move in the same direction around the circle.
When photons of red light fall at right angles to the surface of glass, they will all reflect with the same probability, no photon will have more or less chance that 4%, say.
If electrons were really different, then, when they are captured by the protons to make hydrogen atoms, they would move in different orbit sizes and they would have different energies.
However, there is no experimental evidence of such differences.