These three ships are all in the Gameplay directory and are all in the same xml file. They are in the order in which they appear in the file.

1.  Navigator Commander Ship The Core
The description indicates it gives +1 Antimatter for each survey. It doesn’t.

ShipComponentDefs.xml
Search for surveyantimatter
Scroll down a little to find <Lifetime>Target</Lifetime>
Change it to <Lifetime>Instant</Lifetime> to fix the bug.

2.  Onyx Hive Commander Ship Nephelinite
The description indicates it gives +1 Promethion from each battle. It doesn’t. It has the same problem as The Core ship above.

ShipComponentDefs.xml
Search for battlepromethion. It is the next component after the one above.
Scroll down a little to find <Lifetime>Target</Lifetime>
Change it to <Lifetime>Instant</Lifetime> to fix the bug.

The xml indicates it requires a successful battle instead of just a battle. After this fix, I’ve verified that successful battles do give promethion and battles that destroy the Nephelinite don’t give promethion. I haven’t had a battle go more than one round, so I don’t know if or when promethion will be given when a battle goes more than one round.

3.  Terran Alliance Commander Ship Curiosity
The description indicates it gives +1 Research from surveying. I don’t know if it does or not. I doubt that it does because the xml has the same structure as the two previous commander ships, which don’t work right.

ShipComponentDefs.xml
Search for researchpersurvey.
Scroll down a little to find <Lifetime>Target</Lifetime>
Change it to <Lifetime>Instant</Lifetime> to probably fix the bug, assuming it is bugged.

I have tried to verify that it doesn’t work without the “fix” and does work with the “fix”. The amount of research that has been done towards a tech should go up if research is granted when a survey is completed, but I haven’t been able to find anything that indicates how much research has been done towards a tech.

I checked everywhere I could think of in the game’s UI. I also tried a lot of commands in the console to show various stats, but I couldn’t find anything that gave the information.

I could find research in both places, but that was research per turn, which is different.

UPDATED January 29

I have made a mod that gives 100 research from surveying.  I was able to complete 4 or 5 techs after the first survey, so there is no doubt that I received 100 research.  This means there is nothing wrong with this ship's ability.

I have also looked at the xml for this and for the antimatter gained by the Navigator ship shown first.  There are more differences than I indicated.  I'll let someone from Stardock figure out what is actually wrong and how to fix it.

I have confirmed that the Navigator ship doesn't get the antimatter, so it is bugged.

I have found more Commander Ship problems. All of these are in MercenaryComponentDefs.xml.

Festron Commander Ships

Two ships claim to capture ships defeated in battle, but don’t.
The Claw with 25% chance of success.
Charon with 100% chance of success.
I went back to GalCiv3 and the Snathi Revenge DLC to see how capturing/scavenging worked there.

I then modified two scavenging sections to get them to work.

I don’t know if what I did is the best way, but they both work correctly now.

Xeloxi Commander Ships
Lenore’s Wake has 25% chance of capturing ships defeated in battle, but doesn’t capture any. Fixed as noted in Festron Commander ships above.

The next ship is strange.
Killigrew claims it gives +1 Control per battle. It does give the control right after the battle, but the given control vanishes at the beginning of the next turn. This was hard to check, so I modded the value to 10 to make it easier to see in action.

The xml code for this is the same code, except for what is given and the amount, as the xml code that gives +100 Credits per battle.

The Credits don’t vanish like the Control does. I don’t understand why the results are different.

Yes, thank you Old-Spider, your work is always appreciated, and thanks Joe for checking these bugs out. Looking forward to the incoming updates and GC4 Next.

Old-Spider,

I am playing version 1.11.365778 as the Drath Freehold which has a command ship named "Buopoth" which says it has "100% chance to capture ships defeated in battle." as shown in the first screen snapshot below.  As expected, this ability does not work, so I tried to make the modifications you recommended to the file:

 D:\Program Files\Epic Games\GCIVTestEdition\Data\Gameplay\MercenaryComponentDefs.xml

(as shown in the second screen snapshot below).  I restarted to game to make sure it would use the modified file.  However, this ship is still not able to capture enemy ships it defeats in battle.  Did I do something wrong or is there something else I need to do to make this ability work?

Old-Spider,

Thank you for the information that I was missing!  My command ship is now busily capturing enemy ships.  An interesting side effect is that, when I capture a Cutter that was defending a Ship Graveyard, it apparently also gets the ability to capture enemy ships after defeating them in combat.

The only disappointment is that captured ships only have 1 hit point.  This means I have to spend turns healing them before I can use them.  Oh well, it is still an interesting ability and I am glad you provided the information needed to make it work.

Hopefully, the devs will soon fix all of the abilities of command ships that currently do not work.  It does not seem like it would be very hard to do and it would eliminate a large number of complaints about things not working the way they are supposed to.