Okay, I have now pushed commits to flightcrew master to hopefully handle this a bit better.
Instead of silently barfing up an exception and terminating when an url to an external resource is not properly utf-8 encoded, flightcrew will now simply print a a warning to stderr so that the end user knows something is up.
Flightcrew will not report a real error or warning in this case as that path may be a legitimate file path on that external server and it is properly url encoded latin-1.
Here is a result of flightcrew-plugin built with the new code running on an unpacked copy of your problem epub:
This should enable you to track down these strange urls in your code and if needed "fix" them if they even indeed need to be "fixed".
So please pull from flightcrew master and rebuild and let me know if this works better for you.