There is a fix for all 3 of these issues implemented in an upcoming change.
For those who would like to fix it now, or who are using a 'static' code base and are experiencing these issues:
Bot::SavePetStats()
https://github.com/EQEmu/Server/blob.../bot.cpp#L1839
	Code:
	-	return 0;
+	return results.LastInsertedID();
 
Bot::SaveBotGroup()
https://github.com/EQEmu/Server/blob.../bot.cpp#L3483
	Code:
	+	botGroupId = results.LastInsertedID();
	if(botGroupId == 0)