Q - The clean exhaust message comes on than goes off and than a wrench symbol comes on than goes back to exhaust on and on. This is a Ford 2010 250 6.4 diesel

A - I would start by checking to see what trouble codes are in the ecm.  There should be some saved if the wrench light was on.  If it only does it during regen, it could be anything from the DPF filter plugging up to a bad sensor in the exhaust system.  Pulling the codes should give you a pointer in the right direction.