Two widely believed conjectures:
- The proportion of hyperbolic knots amongst prime knots of $n$ or fewer crossings approaches $1$ as $n$ approaches infinity.
- The crossing number (the minimal number of crossings of a knot diagram of that knot) of a composite knot is not less than that of each of its factors.
The first conjecture is widely believed because of massive numerical evidence, and because many topological objects that are related to knots are generically hyperbolic- e.g. compact surfaces, various classes of 3-manifolds, closures of random braids...
The second conjecture is also widely believed to be true because of lots of numerical evidence- it is moreover believed that crossing number should in fact be additive with respect to connect sum (so the crossing number of a composite knot should actually be the sum of the crossing number of its components). It was proved for various classes of knots- alternating knots, adequate knots, torus knots, etc.
... and yet ...Malyutin shows that either Conjecture 1 or Conjecture 2 must be false!!
Update: Malyutin has proven that Conjecture 1 is false. Thus this answer becomes honest, and Conjecture 1 is a conjecture that was widely believed to be true but (much) later shown to be false. arxiv.org/abs/1907.04458