@martinkuk, on 22 January 2012 - 09:58 PM, said in Ships showing up where they shouldn't:
Allies: 101, 13, 55, 50
Enemies: 9, 21, 2
This is the part of the game that I am least familiar with editing. The Class is a high number to try to avoid conflict, the government is allied with itself because I saw numerous other governments do the same, and the other allies and enemies were chosen to attempt to populate the ally/enemy list with roughly the same people as the Federation, so that they would act as police (friends with traders, enemies with pirates, etc).
From a quick look, I believe your problem is that Govt ID 194 "Shards" is part of class 55, which has class 1 set as enemy. Since you are destroying ships that are the ally of the Fed's enemy, they like you.
There might be other conflicts, that is just the first one I found (I started at the bottom of the Govt list since the class numbers were fairly high). If there is a table/list of all classes that would quicken your search and prevent future mistakes.