Charles; that absolutely should not happen and indeed the system simply interrogates redemption booking-class availability on BA-operated flights. There is no way for British Airways to use a different booking class code for seats available to non 2-4-1 redeemers, compared to those with a voucher. For reference, the booking classes are Z for First, U for Club, P for World Traveller Plus and X for Traveller/Domestic. They don’t have, for example, X(Miles) and X(AmEx); it’s X or nothing!
Can you perhaps remember when you last experienced this issue? What was your search method: did you search sectors separately on miles only and then combine when you came to including the 2-4-1 (this can throw things slightly as the single-sector interrogations don’t take into account inter-sector minimum connection times)? If you did sector-check first, are you sure that ba.com did not simply remove some overly-long, or otherwise impractical connections? Though this is very unlikely with LHR, are you positive that the domestic connections were all operated by BA and not code-share or franchise? Was this all on ba.com or did you cross-check with the call centre? Can you replicate the problem today with some sample dates?
If there is a fault then it should certainly be brought to BA’s attention as that’s what it will be: a fault, rather than a policy.
As you might be able to tell, I’ve used BA Miles a lot over the years, so I’ve come across almost every quirk of the system!