So have your replicators approach a system from an unexpected vector; one course correction in interstellar space should be enough. Also I'd expect the probes

So have your replicators approach a system from an unexpected vector; one course correction in interstellar space should be enough. Also I'd expect the probes would communicate with the homeworld via relays (where they were replicated) rather than directly, so it'd take a fair amount of effort to unravel a replicator network unless you caught one of the very first probes. And also it'd be conspicuous if there was a volume of space in your network where your probes always failed.