If you down-scale, vertex-edit, skew, rotate or generally do anything with brushes smaller than 16 or 8 Units or not making them snap to the a grid of this size or higher you can easily drive vbsp insane (causing polygons to come out of nowhere).
Try to remember what you changed/added last since the problem came. Think of any brushes that aren't simple, right-angled walls, floors or ceilings. Try deleting or re-building them.
Like Captain P said, try searching for "invalid solid structure" errors using Hammer's problem finder (Alt-P).
Obviously check the brush that has apparently been "stretched" in game first and consider deleting it and replace it by a new one (fixing some errors that would perhaps be difficult to find).
Why snark works.