Wire nuts can come loose and fall off. It's likely that the burnt wire nut you had, was loose. The landing gear drive motor draws a fair amount of current and if the connection was loose, it would have produced a lot of heat at it. If everything appeared ok, then clip off the burnt part of the wires and strip them. Twist them together with pliers and then screw on the wire nut. Once you've done that, take a length of electrical tape and wrap it around the wire nut down to the pair of wires in the same direction as you screwed on the wire nut. This will prevent the wire nut from vibrating loose over time.
Helen & George VE3INB and Max (Bichon Frise)
2006 Silverado 2500HD D/A,
2006 Cruiser CF30SK