It is not uncommon for apps to use the date and time (including seconds) in log file names to ensure / enforce unique file names. I am sure this is why iFly does it.
In many cases, for the log file to be useful it needs to be copied from the SD card to somewhere else. In those cases, often the date/time stamp is the time the file was copied, not the time the file was originally created.
Personally, I prefer to have the time/date in the filename. If I'm looking for a specific flight, and it's far enough back in history that I don't simply remember the date and time it occurred, I typically reference my logbook first to find the flight, then the date/time in the filename quickly leads to the desired flight.
I fly similar but not-quite-the-same routes frequently, and typically do not save each unique flight plan with a name. Often, the plan changes mid-flight when I get re-vectored by ATC. If iFly tried to pick some version of the flight plan to use in the filename, say maybe the original plan I entered before I started getting revectored, and the file had an ambiguous date on it because I copied it off the SD card to my permanent archive folder, then I might have a hard time figuring out which version was the flight I really wanted.