While we are trying to keep GPGNET compatibility to the max, some things cannot be avoided.
Here is the list of potential problems :
Sorian AI
Problem : Sorian AI is included in FAF, and keeping the AI as a mod will break FA.
Solution : Remove/rename Sorian AI files, and/or only play Sorian AI on FAF.
Units Cap
Problem : FA-FAF lobby is proposing more options for units cap (125, 375, 625 and 875). That is not supported in GPGNET, and so it can crash/hang the lobby on GPGNET if the last game you played on FAF used over 500 as units cap limit.
Solution : Rehost a game on FAF, change the unit cap to 500, and rehost on GPGNET. Or only play on FAF