Well, I can't speak for user-made campaigns, but my explanation is accurate for at least 80% of cases in canon FS1, STR, and FS2.
The Carthage was deployed in a rather strange position...I mean, the Sobek was more than sufficient. They may not have felt threatened enough to deploy fighter squadrons. A single Cain and a few Nephilims should be a piece of cake for the assault fighters already on station. I guess they thought that with the extra firepower, it'd be even less necessary.
The SD Ravana's fighter compliment was likely what you fought in the earlier missions in the Nebula. If you count, it'd be pretty low on fighters by the time it was attacked.
Well, in the main FS2 campaign, the NTD Repulse probably had most of its squadrons going around Epsilon Pegasi, and it decided to take action with only its defensive compliment of a wing or two, because it was to kill a single Leviathan having its way with two Fenris cruisers.
The Aquitaine, probably had its wings on other missions in Proving Grounds...though I kinda doubt this one... (Alpha One saved the day anyway, so no problem here). As noted, it was attacked by the SC Urobach while its wings were likely away on mission.
The NTD Uhuru and NTD Vindicator likely had there attached fighter wings gradually stripped from them as they ran multiple consecutive jump node blockades. Which is why that when they were attacked, they had little left to respond with.
The Pheonecia...well, hell I don't know. Command was smoking crack. Only reason to explain why they expect a Hecate to be able to slow the Sath even one second.
The Beleth had likely used up most of its squadrons assisting the Sathanas. After the destruction of the Ravana, you can assume that most of the fighters you faced came from the Sath or the Beleth.
The Psamtik had its squadrons on other missions, most likely, or didn't see the need to deploy them. (In fact, the Psamtik's own guns are more than sufficient to repel all the fighters and bombers the Shivans throw at it without the player's squadrons interfering). The Sath just jumps in and smokes it. Not a chance to react.
The Beast probably used all its squadrons attacking the GTVA convoys and stuff (though they could have also come from Saths).
The Nebiros was never in any real danger.
The Bastion carried no fighters, since it was decommissioned and as used as a massive meson-bomb carrier.