Major mistakes in accepted FOCS/STOC papers
One case is Blum-Feldman-Micali's STOC '88 paper. The flaw was pointed to them by Mihir Bellare (private communication). You can find the relevant discussion here.
The Petri net reachability problem has a rich history where incomplete or flawed proofs later lead to new results.  G.S. Sacerdote and R.L. Tenney presented an incomplete decidability proof at STOC '77, which was however instrumental in the later proof of E.W. Mayr at STOC '81 and its improvement by S.R. Kosaraju at STOC '82.  These decidability proofs did not come with complexity upper bounds (they employ well quasi-orderings for termination).  Z. Bouziane later claimed to have found a 2ExpSpace algorithm at FOCS '98.  A flaw was pointed by P. Jančar (and finally published in a note), but Bouziane's work has helped renewing the interest into this old question.  Although there are still no known upper bounds on the complexity of this problem, J. Leroux has recently presented a new decidability proof at POPL '11.


Not in STOC/FOCS:



Another case happened in Structure in Complexity Theory (1988) conference (If I'm not mistaken, it's now called Conference on Computational Complexity.) The paper's title was On the power of multi-power interactive protocols. Two years later, the authors (Fortnow, Rompel, and Sipser) published a two-page paper "Errata for On the Power of Multi-Prover Interactive Protocols" in the same conference. Unfortunately, IEEE does not offer this paper for download.