The Military relay is the weak point of this mod at the moment, the effect is hard to understand and lacks good descriptions.
What you noticed was not a bug, but badly explained intended behaviour.
The long description of what this does:
Relay build requirement:
- One military base or high command in the star system
- Patrol HQ, military base or high command on the planet
The relay checks which planets are owned by you and get the highest fleet size of any planet with a relay - regardless of military base /HC location.
The relay always calculates fleet sizes without the current relay bonus, so it might appear that a planet has a larger fleet when that is in fact only due to the relay, which gets ignored for bonus calculation!
It then applies part of that highest fleet size to all planets with a relay, excluding the planet with the highest fleet size. (This is a flat bonus, so any multipliers you have apply to it, which in turn can make the fleet size exceed the planet that has the "original" largest fleet.)
The applied fleet size is calculated as follows, valid for all planets in a star system:
Military base: 20% of highest fleet size applied
High command: 35% of highest fleet size applied
High command with alpha core: 40% of highest fleet size applied
AI core effects work only from a high command, not from a military base.
I am having issues explaining that effect short tooltip, which led to the poor state it is currently in - sorry for that, it's being worked on as the relay gets more love with the next update.