Yup, that's why I included the grade bonus when mentioning their training.

Even if they had no training bonus, however, it would not be enough to explain the dramatic differences.

On one of my training carriers I have the following:

A fighter with a crew grade of 11%, 100% TFT, and a rank two officer with 200 crew training.
A fighter with a crew grade of 2%, 95.3% TFT, and a rank one officer with 50 crew training.
A fighter with a crew grade of 11%, 50.6% TFT, and a rank four officer with 250 crew training.

So you can see why it's not just a matter of a crew grade/training bonus in this case.

In another of my training carriers that was just set to train, all ships are at 0.9% despite several fighters not having any officer at all.

While getting my early fighter carriers up and training with my first generation of fighters, I noticed that a couple of my fighters were sitting at roughly half the TFT rating of the rest of the fighters (The "lowest" of the group have a 2% crew grade and are at 95.3% TFT, while the two apparently bugged fighters each have an 11% crew grade and a 50.6% TFT). Skimming through my other training TGs, I noticed that another carrier was having the same problem: One lone fighter sitting around half the TFT value of the rest of the TG.

The odd thing? All three of my seemingly bugged fighters are commanded by a rank four, commodore level, commander. Not only that, but all of my commodores that are commanding fighters are experiencing the same thing.

Any real explanation for this behavior or is it some odd bug that I've managed to find?