You can select polygons by vertex count. On the right, go to Lists > Statistics > Polygons > By Vertex > hit the little + beside 2, to select all 2-point polygons (or enter the command "select.polygon set vertex psubdiv 2"). Then you can just delete them.
It might of been a poly bevel with "Group Polygons" unselected giving you a local bevel on all the polys - you will get internal faces from that. Another option is duplicating your mesh on top of the old mesh.
Is it possible you've selected those polygons at some point and locked them ("J" by default)? This would make them unselectable and skipped on export (for memory anyway). With nothing selected press I to unlock them if so and then meshcleanup or manually select them again; the best way being with MMB lasso select (which…