I am having several issues with some doors for my mod. I added a new entrance/exit to the Cistern, that leads out into the lake outside Riften. In the creation kit it looks exactly the same as any other door, and I can move between cells using the door marker. But when I save and go to test it in the game the door on the lake on gone, and using the door in the cistern just leads to an empty space where I continually fall.

Second issue I am having deals with the Crypt entrance. Initially I never touched the crypt, leaving it be. The only thing I have done is move the ladder back a few spaces. I can enter the cistern from the crypt. But I can't leave the cistern from the ladder now, I'm not entirely sure if this was before or after moving it. I've always had CTD issues with that door even before the mod, so it took me awhile to figure out that it was actually mod related.

When I looked in the creation kit there are two doors that are inside the cistern that are linked to the crypt ladder.
I am scared to mess around with the crypt doors because they are linked to several quests. I am not experienced at all in the quest department yet, so I've been staying away from it.

I really need help with this.

Thank you in advance for any assistance.

EDIT:
Something is seriously, seriously wrong. Anything connected to the doors is appearing in the cistern in random locations. I just loaded a new save to see if I fixed it, and found the god forsaken mausoleum in my damn doorway. This is incredibly frustrating. At the same time I am laughing my rear off at the sheer randomness of it all.
Anyways, what would cause the linked doors to appear in the cell?

EDIT2: Yes, I read almost all the Creation Kit tutorials. No, I am not a new modder. Yes, I've made successful doors before. There is no obvious reason that any of this should be happening, aside from the quest references attached to these items.

Bump. The doors still just lead me into open space regardless of how correctly they are set up, or they just cause a CTD upon trying to leave the cistern.

Beats me. Some things to perhaps try:

• Did you cut and paste either of the doors? Might they have unexpected scripts attached?
  
• Did one of them get "start game disabled" ticked by mistake?
  
• Does the problem persist if you delete both doors and make a new pair from scratch?
  
• Can you create a pair of working doors anywhere else in the world? Or is the problem widespread?
  
• Did the door teleport marker for the crypt accidentally get dragged into the scenery?

Probably none of them is to blame, but they'll narrow down the problem space a little

I made a small mod awhile back that had working doors just fine, but that was simply for testing a few things. I haven't tried making other doors in this mod aside from those two, but I'll give it a go.
The markers are where I placed them, which is where they were in Vanilla. The problem is that when I save the mod after creating a working door in the Creation Kit, the next time I open the CK the door will be broken. Example:
Ladder exits to crypt, and vice versa. Save, close mod and test. CTD. Open mod again. Ladder now leads to a random teleport marker in Cistern, also CTD.

No matter how many times I delete this random door out in the middle of nowhere, it always, always comes back.

The crypt door and ladder are tied to quests. If I delete these doors will it break the quests? Or simply remove any references to the doors from the quest?

EDIT: I can make doors just fine in other cells. But anything leaving the cistern just creates problems.

As a rule I'd never delete anything from vanilla. I thought you had problems with two new doors giving unexpected results, plus an unexpected effect on the crypt entrance?

A thought occurs to me: have you been editing mods with TESVSnip? It can apparently have all sorts of subtle corruption effects on files.

Another possibility would be to look at the records under details and delete any changes you made to the cistern in your mod. then save and if they stay gone, you can try making the changes again

That would be deleting an entire week of work. Doesn't sound like a lot but it actually is, about 70 hours.
I've stayed away from TESVSnip because I had heard about some of the corruption issues.

The two new doors I was trying to add were giving me problems, but the only reason I had problem to begin with is because the Crypt door suddenly started bugging out. So I thought I would replace the door in an attempt to correct it, but the new crypt door is doing the exact same thing, i.e. dropping you off into oblivion. I am going to attempt deleting the doors on an alternate save of the mod and see if that fixes it.

This is something of a bump. I have some more detailed information for this problem, and noticed something new as well. I can make other doors just fine, but if I use a ladder or a porthole, both Riften types, weird things happened. I am specifically talking about RiftenRWPortholeDoor01 and RiftenRWHallLadderDoor01MinUse. Either of those doors are doing weird things to my mod.
I created a random testing cell, threw in a floor, a regular door and linked that door to a random porthole (the same type as above) that I placed inside the Cistern.
I did this to test whether or not I could make doors leading from the Cistern, and whether they would function properly. I was able to leave the Cistern through this porthole, but when I arrived in the test cell the Mausoleum and one of the light sources were there. I didn't think at the time to check and see if the Mausoleum was still in Riften or if it was just a duplicate. But the light source from the mausoleum was missing when I exited and reloaded the creation kit.
Now, here is the problem. I never placed a mausoleum in that test cell. Never. This is not the first time this has happened. I've actually noticed that anything near or around any porthole or ladder that I touch outside the cistern will appear inside the cistern after saving the Creation Kit.

EDIT: I tend to ramble, so this is the simplest way I can put it. Door A in the Cistern leads to Door B in the Crypt.
Save the creation kit, load up the mod. Door A now says "Open Door to Ragged Flagon Cistern" rather than Riften like it should. CTD or endless fall if I use the door. Reload the creation kit, Door B is no longer in the Crypt, but floating in space (in the same X, Y and Z position as it was in the Crypt), and the Mausoleum is there with it.

I hate bumping topics, but the suggestions given have not fixed this.