It appears ship commands doesn't count ship kills correctly, especially level 3 and 4 skills.

It appears its something to do with ship class and destroying ships you stole/weren't the original owner of.

Game Version

1.7.36

Language

English (EN)

New Game

Yes

Reproduction Steps

1. Purchase perk level 2 in ship command
2. Select a class c ship as your home ship, ensure its one you stole and weren't gifted/bought. The bug still replicates even if you edit the ship to be a class C
3. Assign maximum number of possible crew to your ship
4. Destroy some ships
5. Check skill rank progress

It should be going ip as you kill ships but it doesn't appear to be. Using a class b ship that you acquired/bought appears to make it work better.