How did the reapers never fail a cycle

This will be a decently long reply, and 3 years later but here goes.

The Reapers more or less likely had a twofold reason for leaving evidence of previous civilizations yet clearing out all (or about 95%) of the current advanced population before they leave.  To the first, they're exceptionally destructive and would largely wipe out most of the infrastructure of every single system...almost down to the studs.  But they and their servants do miss things...weapons/tech/structures which may just be beneath their concern, or intentional to guide the development of the next cycle (without a bit of help 50k years may not be enough for their next harvest to do much).  An example on this is the ruins found on mars...humanity was barely able to get out of the Sol system at the time, found a data cache that lead them to discover the dormant mass relay on the edge of the system AND boosted their tech by several hundred years (spoken about in ME1).  Furthermore they still hadn't even finished analyzing it by ME3 so there could have been much more they just hadn't uncovered yet.  Jaavik mentions the previous cycle being the Insuannon i believe that were the Protheans of their time, so leaving behind SOME evidence, just not the 'what the hell happened' seems fairly standard for them. 

As for the population...the game largely infers that the cycles have been going on for at least a billion years, perhaps more.  The Argus of Rho reaper was killed 37 million years prior to the current cycle thats countless (well, i mean figuratively) numbers ago.  The first few cycles largely were a learning curve that *spoiler* the Intelligence was getting his methods and practices in place, not to mention having to build a large enough Reaper fleet to cleanse the galaxy.  Likely the first few dozen cycles weren't every 50k years when you only have 50 or 100 reapers vs current numbers of the 10k, or 100k,  or more of the *.  Or it was at least 50k years between cycles, but again early ones may have taken milennia to fully cleanse the galaxy of its advanced populace until the Reapers could make sufficient numbers of their kind.

However, their goal was the same.  Reduce all advanced life to next to nil, jump back into darkspace, wait until they got the signal for the next cycle to begin.  Vigil explains that agents of the Reapers were left behind to die from exposure or starvation at the end of their cycle...those indoctrinated rapidly that couldn't function anymore without their overlords instructions.  So the Reapers DO leave some populace behind, but aren't concerned about them living long enough to do anything functional since they're all drooling idiots without the masters whip.  Yes, there may be species like the Krogan that can breed faster than the speed of light, but they would absolutely be targeted on a cycle so they wouldn't provide early aid/a greater threat for the next advancing species.  ME3 had Liara seeding planets with time capsules explaining everything, having the blueprints for the crucible, everything the next cycle would need...likely previous cycles couldn't do that or never thought of it (even the Prothean warning on the beacons didn't give any info, just that the Reapers were bad).

And with the repopulating planets, just look at ME1 for Feros.  That was a former prothean planet with lots of structure still available, if little else.  But the colony was there and starting to grow self sufficient before the geth started to set them back.  So even had a planet been horribly irradiated, or largely burned to ash...the next cycle or a few down the road likely had a species that could survive there, or it'd recover enough to be used once more.  Destructive, yes...but planet destroying, no on the Reapers...even with their numbers they don't have that much power (not counting species doing it to themselves or trying to stop an invasion, but the Reapers have a goal and blowing up planets sorta crimps that).