If a wave targets a system with no hostile wormholes, it will spawn from the edge of the system instead. This is generally only possible with exoholes, since you can't take systems without destroying their warp gates. (Note that the exohole itself counts as a hostile wormhole for this, so it can only happen in systems adjacent to an exohole.)
This is why if you're playing against a backdoor hacker it's a good idea to leave at least one hostile system adjacent to every system neighboring your homeworld, or waves will start spawning at random positions in those systems.
As to why you're only getting waves there, either it's bad luck or that's the only system adjacent to a warp gate. It's not 100% clear from your description if that's the case or not.