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(covers information from several alternate timelines)
In 2154, while trapped aboard a Romulan drone ship, Commander Charles Tucker was able to locate the vessel's warp matrix and disable the main coupling, successfully deactivating the ship's warp drive. (ENT: "United")
Later that year, the Enterprise NX-01's warp matrix was compromised by a Klingon subroutine, which infiltrated the ship's command protocols. The subroutine locked open Enterprise's antimatter flow regulators, causing the plasma pressure in the intermix chamber to rise uncontrollably, forcing the crew to increase their speed to dangerously high levels, until Commander Tucker was able to perform a manual shutdown and restart, successfully purging the subroutines from the matrix. (ENT: "Affliction", "Divergence")
In 2375, upon deciding to accept a position at Starfleet Academy as a Professor of Engineering, Deep Space 9's chief of operations Miles O'Brien joked with Dr. Julian Bashir that "somebody has to teach you officers the difference between a warp matrix flux capacitor and a self-sealing stem bolt. " (DS9: "What You Leave Behind")
Later that year, while engaged in combat with the USS Voyager, Ranek, captain of a Lokirrim warship, tied his ship's shields directly into the warp matrix, gambling that the Voyager crew would not willingly open fire, an act which would trigger a core breach. (VOY: "Body and Soul")
In an alternate timeline in 2390, the Delta Flyer experienced an overload in its warp matrix, the result of battle damage with the USS Challenger, which ultimately resulted in the Flyer's destruction due to a core breach. The timeline in which these events occurred was eventually negated when Harry Kim was able to send a message back in time, averting a disaster which destroyed Voyager in 2375. (VOY: "Timeless")