On rotation, the face of the unprecedentedly-large fan and nacelle intake was tilted to the airflow, which caused unexpected changes to the engine.
Nothing should have been unexpected. .. surge at high alpha has always been a design case... and one particularly requiring flight test clearance! Nasty and deadly surge on approach caused several fatals contributing to the record brraking protracted development of the F-111 I believe.
Harryman, that surge had nothing to do with the inlet. It was related to distortion of the engine due to the various G and gyroscopic forces the engine experiences at rotation, which in turn distorted the compressor case resulting in a compressor stall. Pratt claimed afterward that they did have a ground test scheduled that would have uncovered the problem...
That being said, Boeing now has documented procedures that dictate flying test bed testing will be completed prior to installing new (or significantly modified) engines cross wing on a new airplane.