This happens once in a while on my Windows SDK (even when I don't have any antivirus or similar programs running, execute the SDK-Manager as an administrator and so on).
I just update the tools by hand in this case. Which means close the SDK-Manager after the error and open the ANDROID_SDK emp folder. There should be a zip named tools_R16.zip or similar (don't remember the exact name). Unzip that. You should end up with a tools folder. Copy all the files from this folder into ANDROID_SDK ools. Overwrite when asked. And take a backup of the SDKs tools folder beforehand, just in case something explodes.
After that, start the SDK-Manager again. The tools version should be updated.