1) blocking GPS. 2) Electronic noise (mostly the same as blocking GPS, but needs lots more power) 3) thin nets. (bonus points for barrage balloons) 4) shotguns 5) flak (air burst anti-air shells 6) rain
Off the shelf quadcopters are fragile and not designed to cope with hostile flight. Loose a motor and your falling out of the sky.
Loose a GPS track and you'll either hover, or descend. This could be hacked to rely on dead reckoning, but that's inherently inaccurate. the sensors are designed to tell you what way up you are, how fast you are deviating from desired angle, they rarely have odometers.
A small > 250watt narrow band transmitter, Something with harmonics for 2.4gigs, or just a modified microwave magnetron with a decent directional antenna will destroy most hardware.
A thin fishing net is thin, light, cheap and almost invisible. The hardest part is keeping it in the correct place.