Intelligent Design is just the God of the Gaps dressed up in scientific-sounding language. It collects the unanswered questions in biology and says, "We do not know how this happened, therefore an intelligence was involved." And of course if you dig deeply enough, "an intelligence" is almost always Yahweh, father of Jesus Christ, although they often try to keep that quiet in order to appear more objective.
There are two basic categories of contradictory facts for ID: there are things like the flaws we're talking about here, which say "this could not be intelligence" and there are direct attacks on the gaps, where unexplained things like the emergence of "irreducibly complex" features are explained naturalistically. Intelligent Design deals with both easily. The former can be dismissed by just saying that the intelligence wasn't involved in that particular bit. Or it can just be ignored, which seems to be the standard reaction. Any resource that discusses evolution will discuss unanswered questions and problems with the theory. Resources for intelligent design, as far as I can find, also discuss unanswered questions and problems with evolution but make no mention of any potential problems with ID. The latter can be dismissed by just moving on and continuing to object to other gaps. Or, as often happens, it can be dismissed by labeling the scientist as an anti-religious bigot.
There is literally no imaginable discovery that could overturn intelligent design. There are many imaginable discoveries that could overturn evolution. That's fundamentally what makes the latter scientific and the former not.