So, you have a mod that alters a cell, and the interior is unfortunately is a mess with objects clipping through other objects.
This may be because of a mid game addition, or an accident.

Warning, resetting interiors should not be done lightly!

Make sure you have no active quests that are associated with the cell(s) in question.

In this example, we are using the unfortunate problem with my 1.51 update to Wind District Breezehome - Reborn, which caused many issues due to a save quirk when I was updating it.

If you are having this problem, strip your player home completely.  In this case, all displays and storage in Wind District Breezehome - Reborn, Attic, Main House, and Basement, including plants.  Make sure to remove everything, I cannot stress this enough.  Using a "cheat"  mod that allows you to carry everything is helpful. 

Make a hard save.

If you have access to another house, move your family there temporarily. 

Make another save.

Go to Proventus, purchase back the "Alchemy Lab" (aka guest room).

Save again.

Go to a place far far away from the Breezehome interior cells.  Preferably alone.

Save once more.

--->  Now for the really dangerous part.

Exit the game, download the latest update (of Wind districtbreezehome - Reborn).  Install

Re enter the game.

Open Console:

type PCB 

===This purges the cell Buffer.

Save.

Then type:  Resetinterior AAABreezehomeAttic  (enter)

Next:  Resetinterior WhiterunBreezehome  (enter)

Also:  Resetinterior AAABreezehomePlantPeople (enter)

Then: Resetinterior AAABreezehomeBasement (enter)

Close Console.

Another Save.

Exit and Re enter game.

If you  can, wait 30 days in game. (There are several mods that can speed this up).

If everything went alright, the three interior cells of Breezehome should now be totally reset to their "Start" position and the displays and all associated containers are also reset.  Same with the plants.

Hopefully this helps.