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
