It seems that having a level 5 Cleric with Extra Turning & Great Fortitude and then leveling up as the Doomguide Prestige at level 6, makes it impossible to take the Weapon Focus (martial) feat if you don't already have it.

You're given Weapon Focus (exotic) as a level 1 Doomguide but (martial) disappears and can no longer be selected, making martial weapons permanently unavailable to use.

Can anyone else reproduce this bug?

I think you mean Martial Weapons proficiency; there is no Weapon Focus: Martial or Weapon Focus: Exotic feat in the game.

You cannot take the feat as a Doomguide (i.e., on a Doomguide level up). You can take the feat on a Cleric level up, regardless of whether you have Doomguide (or other classes) levelled.

Yes, that's technically a bug, since Martial Weapons proficiency is supposed to have no prerequisites, but you can work around it. The feat is not "permanently unavailable" unless you exclusively level as a Doomguide from that point forward.

You might consider suggesting this as a bug fix for the Community Fixes on the new Neverwinter Vault.

Oops. Yes, I did mean that. Thanks for the clarification. :)