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This happened to me this morning, twice.  (APM 2.5 w/ external gps/mag).

The first time, I flew to the end of the soccer field in Alt Hold mode.  I then flipped the RTL to ON.  It ascended to altitude and returned home. When got back home, it descended but then stopped an hovered at about 50 feet.  I let it stay there for about 10 or 15 seconds, thinking it was trying to make up its mind. After that, I disengaged RTL and landed manually.  

I did about 6 RTL tests. All but two worked perfectly, landed within a meter of where it was Armed.

Anyone have an idea on why this might happen?

Thanks

Bill