Actually, we have no idea what Wesley retrieved in "Peak Performance". LaForge said the Hathaway
already had some dilithium fragments, but there was zero antimatter aboard. It's therefore quite likely that Wesley went back to get either antimatter or then something that will make do as a replacement fuel for starships.
Replicating fuel makes no sense, unless the process is so efficient that it generates more fuel than it consumes (or at least as much), or creates a fuel type that cannot be used for powering the replication but is otherwise needed. It's difficult to see how antimatter could be replicated efficiently (although the TNG Tech Manual suggests there does exist a technology that can do it cheaper than E=mcc, by "flipping" normal matter), and it's good for drama that such "perpetual motion engines" are not indicated to be routine for the Star Trek universe. OTOH, replicators might well require antimatter power to be useful, meaning LaForge and pals would have to try out something else to reinvigorate the [i[Stargazer[/i].
The idea that everything can be replicated but many things shouldn't is still dramatically valid...