Stereoscopic medical videos are recorded, e.g., in stereo endoscopy or during video recording medical/dental operations. This paper examines quality issues in the recorded stereoscopic medical videos, as insufficient quality may induce visual fatigue to doctors. No attention has been paid to stereo quality and ensuing fatigue issues in the scientific literature so far. Two of the most commonly encountered quality issues in stereoscopic data, namely stereoscopic window violations and bent windows, were searched for in stereo endoscopic medical videos. Furthermore, an additional stereo quality issue encountered in dental operation videos, namely excessive disparity, was detected and fixed. The conducted experiments prove the existence of such quality issues in stereoscopic medical data and highlight the need for their detection and correction.