Pretty much we live in a Rural/Farming Community, but several times in areas of seemingly no interest (farm field, wooded area) my wife and I both have witnessed what appears to be a small craft with white and red/green nav lights off the road well after 10:00 at night......The only reason I could think of for seeing these up there, so late and with nothing really note worthy would be coyote hunters, but most of those guys run Dogs and you kind of know they're out there.
Any ideas?

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Most likely a crop duster. They spray in the off hours before, and after midnight. Bugs are dormant at that time.  

Didn't think of that...
The last one I saw I'm 99% sure was a small "drone" (size, altitude, lights, speed) it was just odd for it to be out at 10:00 at night and the nearest house almost a mile away.

They used to run light aircraft (182's) where I grew up with thermals late at night to look for grow operations.  Evidently the grow lights put off lots of heat so nighttime was the best time to look for them.

Years back, I heard about the DEA and Local Po-Po flying around looking for heat signatures: They showed a Thermal picture on the evening News showing  someones Roof and clearly there were some rather significant hot spots in a pattern.....yea, it wasn't the light someone left on in the Attic.