I'm not 100% sure this is a beta thing, but I don't remember seeing it outside the beta.
When playing as the Vasari, I've noticed that the pathfinding randomly decides that phase stabilizers don't exist. A typical example is that I want to move a fleet from A to B, both of which are stabilizer nodes (they have the green "phase stabilizer node" text, the structures exist, etc). When I click on B, though, the computer displays a route that takes them from A via phase lanes to C, through a stabilizer to D, then through phase lanes again to reach B. This does not seem correct to me.
The only commonality I've been able to come up with is that I *think* that in all cases, I moved the fleet into system A before creating the stabilizer node (whether I created it by building a phase gate, by upgrading a starbase, or by using the Marauder's ability). But I doubt that's a complete explanation. Has anyone else seen this behavior?