Yes I've seen that error many times too; usually it's when I've been connected to an ECU and then it has gone out of range (WiFi connection) and then come back and reconnected. I'm not sure if it relates to some peculiarity of the WiFi connector, my custom package or some unusual behaviour in Tune.
I've also had the odd strange situation with something throwing up a number of faults when compiling (not picked up in Validation stage) that magically go away if you close and reopen Build, or faults sending packages that fix themselves either by re-sending or just recompiling with a trivial change in Build. I guess that's it's not surprising to find the odd bug like these, and given my overall extremely happy feelings toward the whole Build/Tune system I don't let it upset me too much