Parts locked when in fairing.

[Jsythere-Eighty-Niner]

I've made a rocket that has more than one stage. The second stage's engine is encased within a fairing attatched to the top of the first stage, acting as an interstage, and closing at the bottom of the second stage's fuel tank. When I first close the fairing after building it and launch the rocket, the two stages separate flawlessly. But upon loading the rocket up for a second time as a subassembly, the two stages won't separate as the fairing is holding them together, locking the second stage's engine with an invisible force within the interstage fairing. The two stages are both separate spacecraft at this point, but they still remain connected by the fairing. If I were to timewarp and clip through the fairing, it will warp the upper half of the rocket back to its place within the fairing and destroy it instantly. 

Here are some pictures to help visualize my issue...

Second stage engine housed inside interstage fairing of the first stage.

First time loaded, they separate.

(Added as a subassembly to a payload) The bottom stage is now a separate craft and is separated, but they remain stuck together by the fairing in the middle. The only way to break the link would be deploying the fairing, but the first stage has no probe core, so that is impossible. (The insterstage isn't supposed to be deployed, and is to remain intact.)

Timewarp does help temporarily, but will cause the rocket to spontaneously combust when time is reverted to normal.

Is it normal for a part to become stuck within a fairing if it isn't deployed?

 

[OHara]

About a year ago, a bug appeared that sometimes makes fairings not let go, https://bugs.kerbalspaceprogram.com/issues/21915
It appeared when Squad implemented a feature-request to keep the deploy mechanism active on fairings between stages, and now it seems we are stuck with it.

The reason it sounds like you hit this bug is that it depends on where the 'root' part is relative to the decoupler inside the fairing.  The root part is the first one you place. When sections of the rocket separate KSP follows the section with the root part. You can change the root part with the fourth button in the upper left of the VAB screen, after 'offset' and 'rotate'

If that is the problem causing you trouble, then the workarounds are:
+ After decoupling, right-click on the fairing and select 'Deploy' so that the fairing separates into pieces, or
+ Quicksave and quickload, F5/F9, or
+ While still in the VAB, change the 'root part' to something above the decoupler

[Rhomphaia]

From my understanding, the root part should already be above the decoupler in this case.  testing myself the behavior I experienced felt a lot like a milder version of another bug with broken solar panels

https://bugs.kerbalspaceprogram.com/issues/24913

 

the first time I experienced that particular bug it reminded me of an even older bug with fairings

https://bugs.kerbalspaceprogram.com/issues/5149