Yes, there are missing sound effects from the games of the series. They all have minor issues:
MMX: missing voice clip for Hadoken
MMX2: broken HDMA fade-in effect in Centipede's stage
MMX3: saturn version, so you can skip all maverick stages
MMX4-X6: all sound was reprocessed DOWN, and the volume reduced. this lowered the overall music quality.
MMX6: broken timers for all destructables in Metal Shark Player's stage
MMX6: broken timer for Gate, when he moves right to left and turns around