Since i don't have time to test by myself right now, please let me know which dungeons have that issue and which doors (and mechanisms if there's any), i'll check as soon as i can.
Oh, it's easy, any dungeon starting with Bastion of Lok (level 20) and ending with level 58 I think (Labyrinth of Terror/Ebony Tower). All doors that should be open with an mechanism or by killing mobs are open by default, no exception.
Here is DynamicGeo_9093.xml, I believe it's Akasha's Hideout. This dungeon has several doors that you have to open either by killing mobs or using a mechanism.
<?xml version="1.0" encoding="utf-8"?>
<DynamicGeoData continentId="9093">
<DoorList>
<!-- 사교도의 은신처 asw_c_SD -->
<Door id="909301" name="AEN_A_SD_Door_001" desc="아카샤의 은신처 문 01" auto="false" closedMSec="99999000" openMSec="-1" pos="66090,127143,512" scale="0.68" dir="90" bottomLeftPos="66149,127143,512" bottomRightPos="66025,127143,512" height="180" mesh="NPC_SteelDoor.Skel.NPC_SteelDoor_Skel" phat="NPC_SteelDoor.Physics.NPC_SteelDoor_Skel_Physics" animSet="NPC_SteelDoor_ANI.Anim.NPC_SteelDoor_Anim" animTree="S1Prototype.SimpleAnimTree" />
<Door id="909302" name="AEN_A_SD_Door_002" desc="아카샤의 은신처 문 02" auto="false" closedMSec="99999000" openMSec="-1" pos="66090,129863,512" scale="0.68" dir="90" bottomLeftPos="66149,129865,512" bottomRightPos="66025,129865,512" height="180" mesh="NPC_SteelDoor.Skel.NPC_SteelDoor_Skel" phat="NPC_SteelDoor.Physics.NPC_SteelDoor_Skel_Physics" animSet="NPC_SteelDoor_ANI.Anim.NPC_SteelDoor_Anim" animTree="S1Prototype.SimpleAnimTree" />
<Door id="909303" name="AEN_A_SD_Door_003" desc="아카샤의 은신처 문 03" auto="false" closedMSec="99999000" openMSec="-1" pos="68018,131684,0" scale="1" dir="0" bottomLeftPos="68016,131494,0" bottomRightPos="68016,131862,0" height="500" mesh="NPC_Door.Skel.NPC_AEN_Door_Skel" phat="NPC_Door.Physics.NPC_AEN_Door_Skel_Physics" animSet="NPC_Door_ANI.Anim.NPC_AEN_Door_Anim" animTree="S1Prototype.SimpleAnimTree" />
<Door id="909304" name="AEN_A_SD_Door_004" desc="아카샤의 은신처 문 04" auto="false" closedMSec="99999000" openMSec="-1" pos="69205,130485,0" scale="1" dir="90" bottomLeftPos="69402,130488,0" bottomRightPos="69030,130488,0" height="500" mesh="NPC_Door.Skel.NPC_AEN_Door_Skel" phat="NPC_Door.Physics.NPC_AEN_Door_Skel_Physics" animSet="NPC_Door_ANI.Anim.NPC_AEN_Door_Anim" animTree="S1Prototype.SimpleAnimTree" />
<Door id="909305" name="AEN_A_SD_Door_005" desc="아카샤의 은신처 문 05" auto="false" closedMSec="99999000" openMSec="-1" pos="69205,132954,0" scale="1" dir="90" bottomLeftPos="69402,132956,0" bottomRightPos="69030,132956,0" height="500" mesh="NPC_Door.Skel.NPC_AEN_Door_Skel" phat="NPC_Door.Physics.NPC_AEN_Door_Skel_Physics" animSet="NPC_Door_ANI.Anim.NPC_AEN_Door_Anim" animTree="S1Prototype.SimpleAnimTree" />
<Door id="909306" name="AEN_A_SD_Door_006" desc="아카샤의 은신처 문 06" auto="false" closedMSec="99999000" openMSec="-1" pos="70478,131691,0" scale="1" dir="0" bottomLeftPos="70478,131494,0" bottomRightPos="70478,131862,0" height="500" mesh="NPC_Door.Skel.NPC_AEN_Door_Skel" phat="NPC_Door.Physics.NPC_AEN_Door_Skel_Physics" animSet="NPC_Door_ANI.Anim.NPC_AEN_Door_Anim" animTree="S1Prototype.SimpleAnimTree" />
</DoorList>
<ShuttleList>
</ShuttleList>
</DynamicGeoData>