Then it should be.
The mod need to check the status of these special buildings in some cases to active a script, that could reach some functions the base game cannot achieve. These information are recorded while constructing. If other mods say: “Oh I don’t want to tell you what im doing now”, then these information are lost.
When you destroy these entities, the game will try to reset the effects of them (such as the error you feedback: clear the beacon covered area). If the destroyed entity doesn’t have recorded information during the construction stage, the error occurs.
There is a simple method to check whether the buildings successfully created under this mod series: The Construction Animation.
If you don’t see the animation, the building is probably created by a silent raised script which won’t detected by this mod. This will cause error.
The crash may not happen when the error occurs, but these issued entities aren’t able to achieve some of their special functions, they are fake entities.(psychic beacon won’t share any bonus to military entities surrounds, detector has no alert scope to slowdown enemies, radar never send the spotter, chrono sphere refuse players’ calling …)
I’m sorry that this bug cannot be fixed due to mod compatibility, you may need to change the mod list, disable this mod, or just pay attention to these special buildings, don’t build them by the issued mod.:-(