This is a starting list of all consistent bugs with the Fallout 3 SDK, the G.E.C.K. You should only read this if you plan on modding Fallout 3 using the G.E.C.K. This also contains information which, while not technically a "Bug" may not be immediately obvious and can be harmful if unknown.
Right-clicking or double-clicking on a form list or blank space in a leveled list will cause the G.E.C.K. to CTD. The solution is to not right-click on a form list or to use the G.E.C.K. power-up mod seen below. (Link #2)
While loading large quantities of files (Such as clicking the category "All" with filtering), the G.E.C.K. may appear to have stopped working. It is fine and will resume working shortly, unless you click it during this time. Then, it will crash. Again, the solution is not to click during this time. There is no fix at this time.
Similarly, due to the prodigious quantity of memory the G.E.C.K. uses, doing something strenuous--such as generating LOD for a large worldspace or auto-navmeshing--will cause it to crash, or, in extreme cases, bluescreen. Whether this happens or not is entirely dependent on the capabilities of your system, although I cannot think of a rig that would be capable of re-doing the LOD for the entire wasteland. No known work-around. Try finding a friend with a better computer to help you.
Attempting to add in or delete an actor value will cause errors. For some, there is a warning message and it doesn't work. For others, this crashes the G.E.C.K.. As of this time, there is no way around this--not even by using tessnip or Fo3edit. It is simply something that must be worked around.
When handling new radio sounds, the G.E.C.K. WILL CTD unless you have a microphone plugged in. No idea, but be sure to do it.
Also, due to the relative instability of the gamebryo engine, the G.E.C.K. will often CTD without cause. There is no solution, so save often.
Resizing the render window with a cell loaded may crash, or it may not. No fix.
Many times, when loading in .nif file, the G.E.C.K. will show the surfaces as red or the same texture of the surrounding surfaces. This is supposed to be indicative of missing or wrongly filed textures, and that is often the cause. However, just as often, the textures are fine, they appear fine in-game, and the G.E.C.K. is just being screwy. There are two solutions: The first is to learn how to set textures properly, so that you know you aren't making mistakes. See link #1. The second solution, which you should really do anyway, is to test your models in-game. If the texture is good (You may need archive invalidated)it's good. If it isn't, it isn't, and this is really the only way to be sure. Also, be sure you delete the model from in-game if it's not supposed to be there.
Once something is deleted, it's permanently deleted. You cannot interact with it. All references to it in-game are gone. Any script referencing it will CTD when run until it's been re-written. The only way to undo a deleted object is to use Fo3edit or restore a former version of the file. Using the former method, you may have to re-add all of the references. Although, if you want to remove all references of something, deleting and the un-deleting with Fo3edit is a pretty good way to do it.
Often, a weapon may not appear to have the same damage in-game as it does in the G.E.C.K.. I assure you, the value is the same. I don't know why this is, but don't sweat it. This can be half-fixed by link #3.
Furthermore, running a fullscreen program such as Fallout may cause objects in the render/preview window to become seemingly transparent, with you being able to see some objects through others. One way to fix this is to toggle the 'Brighten Lights' button until the glitch is stopped.
Having a file with an .esp file as a master is, in principle, fine. However, if you attempt to reference anything from that .esp file, things go horribly, horribly, wrong. Instead of changing the record that you are referencing, it will clone that record with the same ID and possibly form ID but with the new data. You have been warned--ESMify your files, kids!
Personal or common experience
For fixing textures: http://wiki.tesnexus.com/index.php/How_to_fix_hard-coded_texture_paths_in_NIF_files
The power-up mod: http://www.fallout3nexus.com/downloads/file.php?id=15067
Weapon scanner: http://www.fallout3nexus.com/downloads/file.php?id=8323