In a recent game I was playing halfway when in 1600 AD this messgae appeared: File not found -C:\Atari\Units\Guerilla\fortify. and the game would crash. It seems that the guerilla file isn't even in the directory, but I can still create guerilla units.

Have you patched your game installation?

Is there an extension on that file? Is it fortify.wav?

Looks like there is something wrong with your Guerilla.ini file. Look in C:\atari\unites\guerilla\ folder, and open the guerill.ini file.

Look for a line like the following:
[Animations]
BLANK=
DEFAULT=x_Guerilla default.flc
WALK=
RUN=x_Guerilla run.flc
ATTACK1=x_Guerilla attack_a.flc
ATTACK2=x_Guerilla attack_b.flc
ATTACK3=
DEFEND=
DEATH=x_Guerilla death.flc
DEAD=
FORTIFY=x_Guerilla fortify.flc

If its the .wav file, then look for this:

[Sound Effects]
BLANK=
DEFAULT=
WALK=
RUN=GuerillaRun.amb
ATTACK1=GuerillaAttackA.amb
ATTACK2=GuerillaAttackB.amb
ATTACK3=
DEFEND=
DEATH=GuerillaDeath.wav
DEAD=
FORTIFY=GuerillaFortify.wav

Make sure the lines actully correspond to files that are in the directory.

The problem here is that the Guerilla file isn't even there..