Flecks are a mysterious electromagnetic weapon used by the Pure Ones. They are small naturally occurring fragments made of an unknown metallic substance. They are harmless by themselves, but in large quantities remotely effect the gizzards of owls, presumably causing debilitating pain.
Legend of the Guardians: The Owls of Ga'Hoole
After being kidnapped by the Pure Ones and taken to St. Aegolius Academy for Orphaned Owls, Soren, Gylfie and all other non-Tyto owlets are forced to be pickers. Jatt and Jutt explain to the moon blinked owlets how to pick flecks from owl pellets. They have Soren show the owlets where to put the flecks by having him deposit one in a basket filled with flecks. Soren in pulled in by the flecks and succumbs to their power, and a bat takes the fleck out of his beak and puts it in the basket. The seesaw scale the basket is resting on goes down, signalling that the basket is full. A large fruit bat flies in, grabs the basket and flies away with it. Soren walks back to Gylfie gasping.
The scene cuts to The Beaks, where two owls - later revealed to be Metal Beak and Allomere - overlook multiple fruit bats depositing their flecks into an even bigger fleck holding contraption. Metal Beak explains to Allomere that the flecks will be used to make a trap.
When Allomere is sent by the parlimwnt to St. Aegolius to investigate Soren's claims, he and his two fellow Guardians follow a small swarm of bats to The Beaks where the fleck trap has been constructed. The two other Guardians are lured into the middle of the trap by dummies wearing Pure One helmets. Bats activate the trap, releasing the power of the flecks, and the two Guardians are ensnared.
When all the Guardians fly to The Beaks to battle the Pure Ones, they are lured into the trap after trying to protect a group of moon blinked owlets. The trap is activated and renders the Guardians flightless. Allomere, who knew to abandon the Guardians when the trap was activated, stands near a Metal Beak and Nyra, who are overlooking the trap. Allomere cringes, appearing somewhat regretful of his betrayal. Nyra screeches, calling upon hundreds of vampire bats to fly into the trap and drink the Guardians' blood, causing them to die of blood loss. Nyra had previously explained that bats are not impaired by the flecks' power because, unlike owls, they do not have gizzards. Twilight, Digger and Gylfie manage to hold off the swarm of bats for a little while, while Soren flies into a forest fire in an attempt to light a lantern. Twilight chases a bat into the fleck field, experiencing the unpleasant effect of the flecks but managing to escape. He watches hopelessly as bats fly into the field unhindered, and start closing in on the Guardians.
Soren, successfully lighting the lantern, flies above the fleck trap. He dives headfirst into the fleck field with the flaming lantern, throwing it at one of the three fleck holding contraptions. The lantern explodes, causing the holder to close. The two other holders close as well, containing the flecks and shutting off the trap.
Exactly how flecks work and what affect they have on owls is unknown. Based on the appearance of the structure they create when in large quantities, they appear to be electromagnetic in nature. When large masses of flecks are brought together, they create a glowing structure resembling a magnetic field. While this structure/field appears to be composed of energy, it does not behave like lightning, but rather like a magnetic field. While it does glow, it does not appear to create heat - if it does, it is not hot enough to harm small animals (owls, bats) or burn textiles (the fleck basket in the Pelletorium).
The electromagnetism of the flecks gravitates towards the gizzards of owls. This causes an owl great pain and/or discomfort. If the quantity of flecks is large enough it can debilitate owls to the point where they can't fly or walk. While the effect appears to be very painful, it does not appear to be lethal.
While the properties of the flecks in the movie are different than the properties of flecks in the books, the movie still uses the concept of a Devil's Triangle. When three large collections of flecks are spaced equally apart in the shape of a triangle, their magnetic fields converge. Any owl caught within this field feels the combined force of all three piles of flecks.