Some of the early results on pseudorandom generators and hash functions aren't holding up well, but I think that's just progress. We understand the problem a whole lot better than we did back then.
Perhaps more interesting is the literature on memory models. The original publications of the Java and C11 memory models had lots of flaws, which took many years to fix (and that process might not be totally done). I worry that there are a bunch of published results that are similarly flawed but just haven't gotten as much scrutiny.