In the Voyager episode "Deadlock" Voyager is split into two ships occupying the same space but out of phase with each other. They appear to have split their matter but only one ship (the healthy one) had retained a supply of anti-matter which meant that the anti-proton bursts were only firing in the healthy voyager.
Since the proton bursts were only aimed at the anti-matter, why would the proton bursts from the healthy ship damage the unhealthy one?
Why would the proton bursts affect the unhealthy ship if they were sharing the same anti-matter? Which phase was the anti-matter in?