A warp matrix flux capacitor is a component of Federation starships. The phrase is almost certainly a reference to the famous flux capacitor that drove the time machine in the Back to the Future films.
After telling Julian Bashir he was leaving Deep Space 9 to teach at the Academy, Miles O'Brien jokingly claimed it was because "somebody has to teach you officers the difference between a warp matrix flux capacitor and a self-sealing stembolt". (DS9: "What You Leave Behind")
The phrase is also used in the TNG episode Hollow Pursuits. Lieutenant Barclay is offering hypothetical reasons for one of the anti-grav units' failure, and Wesley Crusher suggests that Barclay check the "flow capacitor;" his interruption flusters the sensitive Barclay somewhat. In the next scene, Barclay visits one of his fantastical Holodeck programs and rants to a simulated Counselor Troi about the encounter: "I knew about the flux capacitor, but I didn't need to hear about it from some 17-year-old kid."
Barclay's misuse of the phrase may be exclusively an in-joke by the writers or actor, or it could be intended to undermine the character's intelligence.