ArmA common errors in configs which you should and need to avoid at all cost.

For example on many many addons (even in BIS material) you'll see this arma.rpt error:

Updating base class ->MGunCore, by ca\weapons\config.bin/cfgWeapons/MGun/

You can avoid this error by not changing the MGun class, instead using your own new class by inheriting from this MGunGore.

Other common errors:

Updating base class ->Default, by ca\anims\characters\config.bin/CfgMovesBasic/DefaultDie/
Updating base class ->Default, by ca\anims\characters\config.bin/CfgMovesMaleSdr/States/Crew/
Updating base class CannonCore->Default, by <addon>\config.bin/CfgWeapons/Cannon30/
Updating base class CAWorld->TAG_baseWorld, by <addon>\config.bin/CfgWorlds/Intro/
Updating base class Civilian->SoldierWB, by <addon>\config.bin/CfgVehicles/SoldierWCaptive/
Updating base class controls->, by <addon>\config.bin/RscDisplayArcadeMap/controls/
Updating base class controls->, by <addon>\config.bin/RscDisplayLoading/Variants/Loading_East1/controls/
Updating base class DefaultClutter->, by <addon>\config.bin/CfgWorlds/Intro/clutter/GrassGeneral/
Updating base class Face1->, by <addon>\config.bin/CfgFaces/Man/Face10/
Updating base class HeavyReammoBox->Land_garaz_s_tankem, by <addon>\config.bin/CfgVehicles/HeavyReammoBoxEast/

All can be avoided by not touching these base classes, just inheriting from them into your own new classes.