...out of LHR and it really bugs me
Really? It really bugs you? I'm just trying to recalibrate the scale for things in life that register even briefly on my "Things That Irritate Me" Radar. You were asked for your Boarding Card at the aircraft door - I assume that a further request for your passport would have generated some sort of psychotic murder spree? Sometimes, I really have to shake my head and wonder...
The UK CAA mandates the checking of Boarding Cards and Security Passes at the aircraft door as part of the Access Control protocols. In the U.S. the TSA applies similar procedures, although in the U.S. they actively "test" using TSA staff (They may also do so in the UK, it's just that I haven't seen it). I don't know what the Malta security protocols are
Hopefully after a few weeks they will just forget about it and not bother.
This tends
not to be how things in aviation work. We don't just make things up to irritate people and the write them on the back of a cigarette packet before losing them somewhere.