It is quite often I am submitting binary, and it does not appear in iTunesConnect. Why? my strategy is that I resubmit it. But it is often that resending does not help. Do you know the reason why Apple does not let it appear?
The binary will appear, but it just takes time. Sometimes it'll be visible within minutes, sometimes a few hours, depending on a range of factors (network bandwidth, server congestion, processing times, etc).
Also, some people don't realise that they need to click on the '+' sign under the Build section. That is, when it's ready, it'll appear and clicking on this reveals the binary.
My personal experience has been that it usually takes about a half hour to appear, but once it did take almost 18hrs. I suspect at present there will be larger than usual demand on Apple's servers, reviewers, etc because many developers are updating apps, not just because of iOS 10 and macOS Sierra, but especially because of Xcode 8.1 and Swift 3.
Also useful is this site for checking average App Store Review times (I know it's not what you're actually asking about, but it's a useful resource nonetheless).