Can you please post your logs as described in the description and also publish your world? Published worlds make it super simple to find the issue.

i guess you mean the "space engineers.log"
since it is overwritten during every restart of the game i lost it, but i can publish my world
it will be aviable soon
btw up on reloading it, the ncf i use for removing ships works fine

So this only happened once? Or does it happen all the time ?

only happens once till now during a game session
just right after i place the deconstruction beacon on the ship and after i activate the ncf which only is assigned for removing

edit: here is the savegame after the video
http://gtm.steamproxy.vip/sharedfiles/filedetails/?id=681436912

Encountering terrible freezes (up to 40 seconds) in the Console window of grids these are attached to. there appears to be a problem with the mod writing to the Console at some point, throwing the following errors in log:

2016-05-10 11:00:53.802 - Thread: 1 -> Logging.WriteLine Error: System.IO.IOException: The process cannot access the file 'C:\Users\x\AppData\Roaming\SpaceEngineers\Storage\655922051.sbm_NaniteConstructionSystem\NaniteConstructionSystem.log' because it is being used by another process.
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy, Boolean useLongPath, Boolean checkHost)
at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
at VRage.FileSystem.MyFileSystem.OpenWrite(String path, FileMode mode)
at Sandbox.ModAPI.MyAPIUtilities.VRage.Game.ModAPI.IMyUtilities.WriteFileInLocalStorage(String file, Type callingType)
at NaniteConstructionSystem.Logging.WriteLine(String text)
2016-05-10 11:00:53.803 - Thread: 1 -> Logging.WriteLine Error: System.IO.IOException: The process cannot access the file 'C:\Users\x\AppData\Roaming\SpaceEngineers\Storage\655922051.sbm_NaniteConstructionSystem\NaniteConstructionSystem.log' because it is being used by another process.
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy, Boolean useLongPath, Boolean checkHost)
at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
at VRage.FileSystem.MyFileSystem.OpenWrite(String path, FileMode mode)
at Sandbox.ModAPI.MyAPIUtilities.VRage.Game.ModAPI.IMyUtilities.WriteFileInLocalStorage(String file, Type callingType)
at NaniteConstructionSystem.Logging.WriteLine(String text)
2016-05-10 11:00:53.803 - Thread: 1 -> Logging.WriteLine Error: System.IO.IOException: The process cannot access the file 'C:\Users\x\AppData\Roaming\SpaceEngineers\Storage\655922051.sbm_NaniteConstructionSystem\NaniteConstructionSystem.log' because it is being used by another process.
at System.IO.__Error.WinIOError(Int32 errorCode, String maybeFullPath)
at System.IO.FileStream.Init(String path, FileMode mode, FileAccess access, Int32 rights, Boolean useRights, FileShare share, Int32 bufferSize, FileOptions options, SECURITY_ATTRIBUTES secAttrs, String msgPath, Boolean bFromProxy, Boolean useLongPath, Boolean checkHost)
at System.IO.FileStream..ctor(String path, FileMode mode, FileAccess access, FileShare share)
at VRage.FileSystem.MyFileSystem.OpenWrite(String path, FileMode mode)
at Sandbox.ModAPI.MyAPIUtilities.VRage.Game.ModAPI.IMyUtilities.WriteFileInLocalStorage(String file, Type callingType)
at NaniteConstructionSystem.Logging.WriteLine(String text)

Hope this helps at all. Note that I have no problems with the Console of any other grid or my own character. As soon as I open the Console of the grid these are on, the above error shows in the log.