Has there ever been a time in history where widely accepted scientific theory became falsified?

What you want (if you haven't already been assigned it) is Kuhn's book "The Structure of Scientific Revolutions." Kuhn's thesis is that science operates under overarching theories he calls "paradigms." Most day-to-day scientific research is "normal" science which basically fills in more and more data under the paradigm. However, it usually happens that there is some data that the paradigm can't explain. If the scientific community is sufficiently troubled by this, someone will eventually propose a new paradigm that accounts for the anomalies, and if the scientific community accepts it, you have scientific "revolution" where the new paradigm dictates the new "normal science."

Probably the best-known example would be Newton's physics overturning Aristotle's, only to be overturned by Einstein's relativity (and quantum mechanics).

Phlogiston theory, Aristotelian mechanics, Pluto the ex-planet, Lamarckian evolution

Here's the thing, the results can be reproducible but the paradigm wrong. For example Aristotle is said to have concluded that the earth does not spin because he dropped a rock from a tower and dropped straight down. If the earth was spinning the trajectory of the rock should have curved, because hey...the earth was moving while the rock was falling. Obviously Aristotle had it wrong, but there was nothing inherently unscientific about his method.

There is (and has always been) a tendency for strong proponents of one theory or another to be so focused that they will ignore, or even falsify, data that does not support their theory, or crate data that does. The whole point of the scientific method is to test the data to confirm or deny the theory. Scientists who try to block testing of their data, but expect unquestioned acceptance of their findings, are suspect.

It is the very fundamentals of science that for a theory to gain acceptance it must be reproducible by others. We have just gone through such an example of this where there was an experimenter who sent a neutrino between Switzerland and Italy and he claimed it had gone faster than the speed of light. According to Einstein's law this was not possible. Further experiments should that Einstein was correct and the experimenters results were flawed. You would be hard put to find false science except for some deliberate fakers hoping to cash in by using quack science.

Another great example of science proving itself is in the Darwinian theory. Darwin himself was a very religious man and it must have been quite shocking for him to conclude it was nature at work and not the hand of God's hand. His theory of evolution is now accepted and there is no sign of it being refuted.

I think the others are noting scientific theories, that were thought to be based on solid evidence, but later proved untrue.

The closest thing to what you seek, I think, is 'Lysenkoism' in the Soviet Union. People were forced to follow the scientific policies of Lysenko, despite the lack of evidence/proof, while those against him were denounced as 'bourgeous' or 'facist' scientists. Lysenkoism was decreed the one true 'Communist' science, and therefore it was pushed on people (especially in the Stalin era); despite the lack of facts to support it.

http://en.wikipedia.org/wiki/Lysenkoism (sorry for the wiki reference, but it describes it well)

alchemy, phrenology, "modern" medicine before germ theory, geocentric theory, flat earth theory, is this the direction you wanted.