I agree with your first paragraph but your second paragraph is quite defeatist. I was involved in a quite few of "premortem" meetings where people think of increasing improbable failure modes and devise strategies for them. It's a useful meeting before larges changes to critical systems are made live. In my opinion, this should totally be a known error.
> Having found an entry and exit point, with the latter being the duplicate and therefore geographically incorrect, the software could not extract a valid UK portion of flight plan between these two points.
It doesn't take much imagination to surmise that perhaps real world data is broken and sometimes you are handed data that doesn't have a valid UK portion of flight plan. Bugs can happen, yes, such as in this case where a valid flight plan was misinterpreted to be invalid, but gracefully dealing with the invalid plan should be a requirement.
> Having found an entry and exit point, with the latter being the duplicate and therefore geographically incorrect, the software could not extract a valid UK portion of flight plan between these two points.
It doesn't take much imagination to surmise that perhaps real world data is broken and sometimes you are handed data that doesn't have a valid UK portion of flight plan. Bugs can happen, yes, such as in this case where a valid flight plan was misinterpreted to be invalid, but gracefully dealing with the invalid plan should be a requirement.