This most happens when a flight is off airways. The system assumes that IFR flights will fly along airways. This is perfectly rational in the rest of Europe but not so in the UK. IN fact, the UK has many pilots who can legally fly IFR as long as they don't fly on the airways.
When I came across this problem, we were at an international airport up north flying to an airfield in the South intending to remain below/ outside airways except for a crossing clearance if available abeam Manchester.
When we called for start, thwe tower informed us that the flight plan was being rejected because of our route. The correct route was xyz (we knew that but given VMC for all except the start, we didn't want to get involved with slot times).
Having explained the situation to the ATCO, we requested that ATC contact IFPS or the local ACC and explain the situation so that a flight plan would be filed for us. Unfortunately, the ATCO was unable to do this for us and the ACC could not help us.
The result.....we "booked out IFR" and once clear and continued as plannned without a flight plan......got our crossing clearance (Thanks)...and arrived safely.
If the UK is going to have this off airways free flight IFR system then it is beholding on the UK to ensure that flights making use of that system are not prevented from having a flight plan active.
Perhaps, we need a note in the UK AIP that off airways flights will be treated as VFR flights when considering flight plans.
Regards,
DFC