Numerous irreducable complexity arguments have been countered. Most of the time the reason science didn't have an answer for them was that no-one had got around to researching that particular thing yet.
The whole "science can't explain it so it must be God*" is bunk. If science can't explain it that simply means either:
- science hasn't got around to explaining it yet
- it's not currently scientifically explainable
Absence of an explanation does NOT imply God (See the "God of the Gaps" argument).
As you correctly point out, a key part of science is to question itself, and evolution theory has undergone numerous changes, clarifications and updates in the light of new evidence or arguments since its inception (obvious example: discovery of DNA).
Anyway, this argument could go on for ages. I suggest you read
http://en.wikipedia.org/wiki/Intelligent_design - especially the "Intelligent design controversy" section. It does a much better job than I can ever do of explaining quite how unscientific ID is - including that ID supporters are trying to get the scientific method redefined to suit them.
*insert other pseudoscientific deity reference here