Good grief, what a mess. None of what is stated here, or obviously in the film, has any basis in reality. The religious and philosophers are constantly looking for "proof" in science not realizing that faith can not be proven. Scientists who should know better get all gooey eyed and launch off on absurd and ridiculous flights of spiritual fancy. Lets set some of this straight.

What the Bleep addresses our notion of "what is reality?" It deals with the subatomic levels of reality and with quantum mechanics and physics in exloring the "true" nature of reality.
Yikes! Science is very limited in what it does. Science does not ask why, even in quantum physics. Science deals with what is there, not why it's there. That's the entire basis of the scientific method. For example, science defines and explains how inertia works. Science never asks why matter has inertia.

When scientists peer into the atom deep enough, they find that there is a level of reality in which all classical physics ceases to exist.
Not true. Classical physics is the level above quantum physics. It is still there! Classical physics got extended, not replaced. Quantum mechanics on the small end, relativity on the large end. In other cases, such as conservation of energy, things work in all scales.

And a new, "quantum" realm begins. At this quantum realm, all is connected. Better yet, all is one. Subatomic particles leap into and out of existence, travel backward in time, even exist in two places at the same time. Conclusions are drawn between real life and this scientific uncovering.
Ouch! This is just waxing poetic from the point of view of people who have never studied quantum mechanics or have become lost in a spiritual bog. Quantum mechanics specifically, and physics in general, goes well beyond the other sciences. Quantum mechanics deals with probabilities and uncertainties. These things seem odd to us because they require that we go well beyond what our limited three dimensional brains can visualize. You must depend upon the mathematics and the experiments. Many people can't make that leap and turn the "strange" world of QM into some spiritual nonsense.

What does this mean to our understanding of reality? Of time, and space? If at the most basic level of life and our being, there are appears to be no time? And the laws of physics are broken seemingly at will?
Laws of physics are not being broken! Time does not disappear! Good grief, QM professors are having heart attacks! You can design a bridge using QM even though it might take years and years of intense calculations. In the end, you will have the same answers as classical mechanics. You can send a rocket into space using classical physics or relativity but, in the end, you get the same answers. Science does not destroy the past, it expands upon it. QM works at a very small scale. Its classical physics with a larger space to work in.

Our mind has the capacity to create reality as it sees fit.
That's why we have the scientific method at all levels of physics.

This "world of infinite possibilities" that exists smaller than the atom can be used consciously to affect our world. Experiments are cited that show how deep meditators are able to raise the ph of water 1 ph by simply setting the intent to do so.
These are all "anecdotal evidence." There has never been a bonafide scientific experiment that shoes this. pH is a macroscopic number, the result of an excess of H or OH molecules. It has absolutely nothing to do with the subatomic.

Machines that are designed to randomly generate numbers mathematically are influenced by people "wishing" that the numbers be scewed a certain way. A Buddhist Monk blesses a cup of water and when it is frozen it creates a dramatically more beauitful ice crystal than water from the same source that is cursed at.
Again, no scientific experiment has ever proved this. It is all based on "look what I saw."

Where science and religion were once one, they split apart in classical times. Religion covered the unseen, science the seen.
They were "one" only because science is relatively recent. The first astonomers were astrologers trying to get their charts right. Aristotle believed he could describe nature just by looking at it (and was wrong on almost all counts for over 2000 years!).

Science describes how things work. Religion and philosophy describe why things work. They were never same thing.

These differences are breaking apart as science and religion (spirituality) are becoming one, once again.
Not unless you completely redeine science and dump the scientific method. This attitude is what causes all the silly nonsense about teaching intelligent design in science classes. Never were the same, never will be the same. They look at completely different things.

The most sacred spiritual truth "We are all One" is now being demonstrated scientifically and there is a whole body of scientific evidence showing that this is true.
There is no such scientific evidence.

This was not meant to be cruel to anyone but this type of nonsense is spreading more and more as education continues to fail in the US. Science is not aribitrary, it is not philosophy, it is not religion, its not a matter of opinion. This is one reason science comes up with answers while the questions of philosophy and religion are no different than they were since the cave man.