Ah yeah! I ran in to something like this but I sent it in as a support email directly. I'll repost what I've seen here for more visibility.
If an engine and its decoupler are in the same stage, or the engine is staged before the decoupler it’s attached to, the decoupler will fail and the ship will be unable to separate.
Activating the engine dumps the shroud, regardless of whether the decoupler has been staged or not. And then the decoupler disappears from staging even though it has not been activated, but the ship does not get separated. If the decoupler fires first all will be well, but if the engine fires first the ship will get borked.
Through testing I also discovered that this only appears to occur with certain decouplers. Like the medium sized TD-25 Stack Decoupler. Other decouplers like the smaller TD-12 do slightly strange things, like teleporting the shroud in front of the ship, but don’t break reality in such a spectacular way. The engine used does not appear to matter.
6/6 Repro is as follows:
-Create a two stage craft using the TD-25 Decoupler
-Move the engine into its own stage, then move the engine stage under the decoupler stage OR move the engine and decoupler into the same stage
-Launch the ship
-When out of fuel, stage, causing the engine to fire before the decoupler
-Observe, the decoupler disappears from staging, but ship is not separated
-Observe decoupler does not appear in parts manager
Once this occurs the ship will be unable to decouple at that point, though other decouplers on the craft do still appear to work.
I went through and tested all the decouplers to see which ones triggered the bug and found the following decouplers reproduce the bug. It appears to affect both decouplers and stack separators from the medium size up. Small and tiny stack separators and decouplers do not reproduce the bug.
Affected parts:
TD-25
TD-37
TD-50
TS-25
TS-37
TS-50
To avoid this bug, keep the decouples in separate stages from the engines, and make sure they stage before the engines.
CiberX15's post in Decouplers not decoupling was marked as the answer