It's controlled by your "logistics" capability -- this is a set total sum of ship logistic sizes that can be in one fleet. To put two fleets in one, drive them to the same square and then click on the "manage" button to the lower left. Then you can click, shift-click a,d etc., on ships to put in the same fleet.

Take a race that has organized or make a custom race with organized. Then take all of the logistics techs + take the logistics specializations. I believe this gives you a maximum of +40 from logistics +10 base +10 from organized for 60 total. I may be missing one more +10 tech so it's either 60 or 70 logistics.

Have you built the Hyperion Logistics System? The level bonus also grants additional logistics (+1 per level).