error message "The file isn’t compatible with QuickTime Player" on file that's already open and playing in QuickTime

Why am I seeing this error message about a file that QuickTime is already playing?

And, if it is a valid error message, why would it appear only when saving the copy file, and not when opening the original?

I believe this is a trapping error bug in the QT X embedded structure since it seems to be repeatable but seemingly only for H.264/AAC default setting encodes in an MOV file container. Basically your CMD-SHIFT-S workflow creates a "temporary" duplicate file from which your use of the "Trim" routine extracts a secondary "temporary" file. Not sure, but suspect QT X is trying to use the "Save As..." routines to copy a portion of the secondary target file data which references the, as yet, unsaved source reference file still in memory which may either be creating a circular reference loop or orphaning/masking the original source data which does exists as an actual file stored on the drive. This does not appear to be a problem for data stored in other file containers or files containing non-H.264/AAC default encodes which automatically trigger the transcoding ("export") of data rather than the "Save As..." routine. For this reason, my guess is that this is a procedural problem based on an error trapping bug that only shows up when using your specific workflow. I normally create a physical "duplicate" file using the Finder CMD-D option on the selected original file stored to the drive and then open the "physical" duplicate copy file in QT X for trimming. This latter approach did not create your issue when I tested it moments ago based on the same originally sourced file. Still you may want to report your specific workflow issue to Apple for correction.