I have also been surprised when I fitted a Marathon + (at 680km into an end-to-end when useless 'Giant PR2' tyre started a sidewall bulge after 6pm with an hour still to ride).
It fitted fine width wise and I I assumed the interference I could hear as I rode the last bit was with my mudguard.
Cut away bottom 6" of the mudguard and all clear. Rolled out (a few yards) at 7am only to find it was still rubbing: my weight made the difference. The M+ was 4mm 'higher' than it was wide and was rubbing under the seatstay bridge. Removed rest of mudguard, and was OK rest of way (to Orkneys). Sold said tyre with 970km on it: looked 'as new' (sold to friend).
Think you'll either have to swap out for a 28 M+ (on rear not ideal) or for another make/model.