Having a similar problem with a 29Meg video file straight off the iPhone. The first time I went to custom crop it, the application segfaulted.
The second time, I went to apply a set of filters (see uploaded images) and the software just hung forever (see uploaded logs). Attempting to cancel items in the queue did nothing.
Curiously, I was able to generate a short preview, but as for actually processing a completed video, it never finished - - just made the fans kick on.
The log is filled with strange messages like endTime must be greater than startTime, FigAssetReader returning err -12780, an assertion failure, a BUG in libdispatch client, a permissions denied on an output file (hold-that-thought), kernel warnings that a thread was caught burning CPU for over 180 second, the app not responding, Perf capability check failing, Decode error (-12903), IQ-CA rejecting report of layer being serviced, unexpected preroll-complete notification, etc.
The save video file when processed in Photoshop (which does video as most folks here know), worked without a hitch. It's not the video file.
(Resuming from the Hold-That-Thought above) -- I think I know where the "bug" is. And I can recreate it.
When I did my first Save As... from the first time I went to run the app, I gave a filename and hit OK believing it would save to the same directory where the source file was. It did not.
In fact, the CPU spun, the system got hot, and the file did not appear -- which is why I went to save again (and hence you see a 1 of 2 in my queue). BTW, it's quite disturbing I can't see what's in the queue (feature request, with queue item cancelation).
When I went to re-save, I saw that it was trying to put it in the root directory, that is /, by default.
This is clearly not allowed by policy, and I suspect the software runs into a problem where it's unaware it got a permission denied. At that point, the queue item isn't removed. (Note, manual removing from the queue doesn't work.)
After quitting the app and restarting (now the third time, and reconstructing the filter chain), I explicitly went out of my way to save to the Desktop.
That worked, actually.
So, I'd recommend trying to repeat the bug: create the default condition of "accidentally" saving to the root directory of the hard drive, and seeing if the problem appears. For me it is repeatable. Saving to the root directory (which I think no one intends to do, but the default start does) puts the software in a tail spin... including not being able to cancel the processing, which is its own separate bug.
El Capitan 10.11.6 using Camerabag Cinema 1.0.600 (NC).