Standard replicators are able to replicate mundane materials and smaller not-too-complex machines. At one point, under the influence of a Cardassian anti-riot program, the replicators in DS9 are magically able to produce something like a self-targetting automatic phaser gun.
Normally, for more complex tasks, such as "building a powerplant" or "making major parts of a starship", very special and rare "industrial" replicators are needed. Apparently, an entire planet normally doesn't have more than half a dozen of these, and they are valuable enough for super secret security measures so the Maquis won't steal them (which they do anyway).
In either case, replication is the process of turning energy into matter.
In addition to their main power supply and thrust, the self-replicating mines contain a standard photon torpedo warhead, which means that they are able to release a considerable amount of energy (which is "gone" after the explosion) from a matter/antimatter reaction. The energy, and of course the antimatter must come from somewhere (regardless of the energy needed, can a replicator replicate antimatter at all?).
It seems improbable (if not impossible) that self-replicating mines could work at all. If you were able to replicate an energy cell containing the same amount of energy as the original one plus a considerable amount of matter/antimatter plus some other stuff, like a cloaking device then you would have the most perfect perpetuum mobile imaginable.
Answer
You're ignoring the fact that each mine contains a small amount of handwavium. In the Trek universe, it's apparently possible to extract reasonable amounts of energy from the vacuum itself and the mass is provided to the relevant mine by its neighbours (who then use the energy they've extracted to create more mass):
The replicator system was designed to accommodate a swarm detonation of up to twenty mines and still maintain the total shell. The replicator was a kludge of Cardassian and Starfleet types and included a raw-matter supply container able to contribute enough mass to build one-sixty-fifth of a complete mine. Mass for any one new mine was transported through the replicator's subspace emitters from as many mines away as was necessary. In a bucket-brigade system. As distributed over the entire shell, enough mass was stored to replace over 2,500 mines.
In the event the mass supply dwindled below 85 percent, the replicator sections were designed to extract particles from the zero-point vacuum domain to replenish the system. The threshold was set deliberately high because of the long lead time required to produce small numbers of particle pairs. - DS9: Technical Manual
Theoretically, the Cardassians could have overwhelmed the system by continually throwing things at the minefield but in practice, the mines can operate indefinitely, replacing broken mines and recharging themselves.
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