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(covers information from several alternate timelines)
In 2293, the Enterprise-B attempted to beam aboard El-Aurian refugees from the SS Lakul, which was caught in the gravimetric field of the Nexus energy ribbon, a conflux of temporal energy, but had trouble locking onto them due to the temporal flux they were experiencing. (Star Trek Generations)
In 2369, Lieutenant Commander Data was able to determine that a quantum singularity lifeform disguised as a Romulan originated from another time continuum, due to a temporal flux in the alien's bioelectric patterns. (TNG: "Timescape")
In an alternate timeline, Tom Paris showed a temporary temporal flux in his nervous system, after he was briefly transported back in time through a subspace fracture on Makull's homeworld, a planet in the Delta Quadrant, in 2371. This timeline was later negated when Captain Janeway, who herself was transported back in time, was able to prevent the accident which caused the subspace fractures to form in the first place. (VOY: "Time and Again")
In another alternate timeline in 2374, the USS Voyager encountered the Krenim, an aggressive Delta Quadrant species which utilized chroniton torpedoes which were able to pass directly through an enemy vessel's shields due to being in a constant state of temporal flux. A torpedo fragment leaked chroniton radiation into the ship, necessitating inoculations for the entire crew. Five years later, the dormant chronitons in Kes's cells would be reactivated by exposure to a biotemporal field, causing her to experience a series of backward time jumps. These time jumps were halted in 2373, when The Doctor exposed Kes to a precisely modulated field of antichronitons to purge her system of the radiation. (VOY: "Before and After")
The weapon ship utilized by the Krenim scientist Annorax existed in a state of temporal flux, essentially existing outside of spacetime. This had the effect of insulating the vessel and all of its occupants from the changes to the timeline initiated by the temporal incursions effected by the crew, and made the ship impervious to conventional weapons. The vessel was kept in a state of temporal flux by it's temporal core. In 2374, when the core was taken offline, the ship phased back into normal space, making it vulnerable to weapons possessed by Voyager. When the temporal core destabilized as a result of massive battle damage, a temporal incursion was initiated within the vessel itself, erasing it and all of its temporal incursions from the timeline. (VOY: "Year of Hell", "Year of Hell, Part II")
In an alternate timeline in 2377, Commander Chakotay was struck by a chronokinetic surge from a spatial rift. His body was thrown into temporal flux, causing him to have the liver of an 80-year-old and the kidneys of a 12-year-old. The Doctor was able to bring him back into temporal realignment with a chroniton-infused serum. This timeline was later negated when Chakotay was able to prevent the accident from occuring by using the navigational deflector to absorb the surge. (VOY: "Shattered")