I often get this and it is nuisance.

Sometimes you can fix it by adding more routing points to your itinerary or changing from price preference to schedule preference.

Quite often B fares allow less stops than M fares or have no stops at a certain transfer point (say fares SIN-US with dual stops in Japan), so M (or then Y) fares could be the only way to accommodate the stop. So be sure you are within the rules and the MPM before trying too hard.