That is perhaps my largest issue with science. On controversial topics, the level of criticism is not equally applied.
It is even worse when we talk about what science filters down to the average voter, as even in cases where the scientists may be fair in their criticism, the public eye is still selective and given unequal weight to certain criticisms.
I thought they do, but they result in spawning new areas of mathematics. Though more often than disagreements, it is questions are are unanswered and either proven unanswerable, or have failed all attempts to achieve an answer. For example, math has been developed for both the outcome that the Riemann hypothesis is true and that it is false. There is sometimes even the fun possibility of these questions being unsolvable and the implications it has if we assume it will eventually be proven a question cannot be answered yes or no (though I can't recall if there are any significant results from assuming such).
My memory is a bit poor on the matter, and my knowledge limited, but I think I've even read of people disagreeing with fundamental concepts in mathematics and attempting to see what happens when you do so. Does it result in a field of math that behaves the same? Does it make working certain problems easier and others harder?
I don't particularly think it's surprising that results from the study of structure end up applying to other disciplines. The wonder of the "unreasonable effectiveness of mathematics" is really that we've managed to find those bits that line up the best between mathematics and other fields.
As long as courts remain within reasonable bounds of "filling in the holes", that is good enough. And we can think about improving the process.