Oh, I see what you mean. The carriers are actually not carrying guardians, but if you kill the guardians prematurely AND there's already a high number of AI ships on the planet the game combines the contents of the carriers into more powerful individual units (retaining the total amount of Strength, but that all depends on whether the Strength values are actually accurate, of course) so that your game doesn't lag to death.
So were you actually shooting the carriers (manually or through the auto-target carriers toggle) or were they deploying by themselves into guardians?
If you just kill all the fleet ships without killing the carriers (the carriers will be untouched if you leave auto-target-carriers off) the carriers should automatically deploy just their normal contents as "room" becomes available.