The centre core is significantly strengthened to cope with the additional load from the side boosters. It also has slightly different aerodynamic properties because of the fixed struts that hold the boosters in place. Either of these could have affected the landing. They'll collect data and fix it.
It didn't actually run out of fuel. It didn't have enough of the hypergolic mix used to ignite the engines (triethylaluminium & triethylborane that causes the green flash sometimes seen at ignition) and only one of the three engines needed for the landing burn re-lit.
