If you play a pragmatic race and use the "cautious" power in your ideology window, you get, as expected, 3 ships per planet. However, once you have done that, it seems the sidebar UI can not cope with so many fleets in a huge galaxy and does not display all the fleets.
Here's the save after the fact:
Older save (pre-ideology)
That last save is quite old, so you will need to play a while to see the bug "in action", or maybe there are cheat codes that give ideology points that you can use to reproduce it "live".
AFAIK, this has been there for a while. I really thought I had reported it, but it seems not, and I haven't played a pragmatic race for a while.
The ideology I'm talking about:
My fleet list, on the right, sorted in descending order of power:
My fleet list in ascending order:
You will notice that my fleets (Dominion Soprano Fleet IV and VI) do not appear in the listing, one way or another. The most powerful fleets are the 3 ships per planets, the less powerful, the scouts&surveys&specials. They are nowhere in the list, so it ain't a sorting order.
I'm guessing there is a hard coded limit for the number of ships to appear and since I have too much, mine have dissapeared.