We are seeing a similar issue. We tend to search for programs and set them to record the series from the Smart Search. We do get to the area where it says it will record it on that channel only, not all channels. However, we are seeing missing episodes. Tonight we found out that it recorded episode 1 of Night Shift but no others. We manually set it in the guide to record episode 6 and record the series from the guide. However it did not pick up episode 7 to be recorded.
I think this is BIG problem. There are some shows that you can find in the Smart Search function that says "Coming Soon". It makes it look like you are setting the series to record, but you get nothing.
Searching and finding shows in the guide to record the series is a pain. It shouldn't be this difficult. We even have some shows in the Series Manager that list the actual channel to the right of the show where it isn't recording any of the shows and indicates (0) when we know there are upcoming shows.