I was very surprised when I first encountered the Mertens conjecture. Define
$$ M(n) = \sum_{k=1}^n \mu(k) $$
The Mertens conjecture was that $|M(n)| < \sqrt{n}$ for $n>1$, in contrast to the Riemann Hypothesis, which is equivalent to $M(n) = O(n^{\frac12 + \epsilon})$ .
The reason I found this conjecture surprising is that it fails heuristically if you assume the Mobius function is randomly $\pm1$ or $0$. The analogue fails with probability $1$ for a random $-1,0,1$ sequence where the nonzero terms have positive density. The law of the iterated logarithm suggests that counterexamples are large but occur with probability 1. So, it doesn't seem surprising that it's false, and that the first counterexamples are uncomfortably large.
There are many heuristics you can use to conjecture that the digits of $\pi$, the distribution of primes, zeros of $\zeta$ etc. seem random. I believe random matrix theory in physics started when people asked whether the properties of particular high-dimensional matrices were special or just what you would expect of random matrices. Sometimes the right random model isn't obvious, and it's not clear to me when to say that an heuristic is reasonable.
On the other hand, if you conjecture that all naturally arising transcendentals have simple continued fractions which appear random, then you would be wrong, since $e = [2;1,2,1,1,4,1,1,6,…,1,1,2n,…]$, and a few numbers algebraically related to $e$ have similar simple continued fraction expansions.
What other plausible conjectures or proven results can be framed as heuristically false according to a reasonable probability model?
Best Answer
I think this example fits, in 1985 H. Maier disproved a very reasonable conjecture on the distribution of prime numbers in short intervals. The probabilistic approach had been thoroughly examined by Harald Cramer. Nice paper by Andrew Granville including this episode in (mathematical) detail, page 23 (or 13 out of 18 in the pdf):
www.dms.umontreal.ca/~andrew/PDF/cramer.pdf