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I have been trying to copy Night of the Museum 2 and at the end of the process I get this message:

Saving 1 titles into directory Z:/MOVIES/Night at the Museum Battle of the Smithsonian
DEBUG: Code 1986 at IB=#@s0c2#N6]wC;_P_:29394781
DEBUG: Code 0 at RJP.'8],Q7]lSQ&Q~Am2:29394321
DEBUG: Code 105560 at RJP.'8],Q7]lSQ&Q~Am2:29393309
LIBMKV_TRACE: Exception: Error while reading input
Failed to save title 0 to file Z:/MOVIES/Night at the Museum Battle of the Smithsonian/title00.mkv
0 titles saved, 1 failed

Any Ideas?

This is a disc mastering error or a new protection. Please submit the full debug log as written by MakeMKV to support@makemkv.com - it should have additional information that is needed for workaround.