The AF points are superimposed onto laser-etched markings on the screen matched to emitters lined up directly above, and of course, any misalignment of the screen will be very obvious. I think a more sinister proposition is that the camera has received a severe knock that has bumped the superimposition emitters out of alignment, but at the very most, such misalignment would manifest as only a little more flare — that is to say, flare that is significantly more noticeable and adverse than normally occurs during the illumination process. The effect has been seen in several well-used and battered EOS 1/1N bodies where the screen has been frequently interchanged.
Warped screen frames are the most common problem where changes have been made hurriedly, clumsily or incompletely — it is a delicate operation with the potential for damage to the screen especially from slippage with the tool, or damage to the frame by forcing an incorrectly seated screen. Irrespective of how much you paid for the camera, a bench examination by a qualified professional is called for now that everybody here has proferred as much as can be without actually physically inspecting the body.