This was seen by several people when the timer first went on sale. I saw it myself a few times when I had an S1. The best we could figure was that it is a software timing bug. If the machine turns off at exactly the right (or maybe wrong time) the machine doesn't turn off all the lamps. However, it causes no problems and you probably won't see it happen again for a long time.
Interestingly, you're the first one to report it here in at least a couple of years, so it is a pretty rare occurrence. BTW: When it happened to me, I saw it maybe three times in two years.
LM GS/3 & LaSpaziale Dream
Mazzer Kony E, Customized Rocky