There are a couple of gotchas with recording conflicts that aren't all that apparent to the new user.
1) Major net shows in particular (and some on FX and others) do not always adhere to regular start/stop times. ABC and NBC seem to be the worst, scheduling shows as "1:01" and ":59" to fill a two-hour block. "The Shield" on FX can sometimes run 4-9 minutes into the next hour, for instance. "Sanctuary" (tonight's premiere) runs 2:02, meaning it will conflict with a double recording scheduled 2 hours afterwards.
2) If you have padded a show for a series link or otherwise, it can also cause a similar conflict. For instance, I normally pad "'Til Death" because FOX runs it a little over. Once they started airing two versions back to back (after dropping the dreadful "Do Not Disturb" after 3 pitiful airings), that meant that it actually conflicted with itself (the first airing overlapping the second) and another recording on another channel.
It's always good to check these things first when a recording appears to not be scheduled that you feel should be, and usually these reasons are why. It's also good to check this ahead of time rather than to figure out why something did not record after the fact.