If I am not mistaken, The Playstation and Saturn versions of MK2 had issues with Shang Tsung morphs as well. Most of the CD versions have the option to disable his morphs during matches.
It is one of the common gameplay compromises that MK games had to make on early CD-ROM based consoles. The N64 Mortal Kombat Trilogy never had that issue. Neither did the 32x version.
The PC versions didn't if you installed the games to HDD? The Saturn could have solved this issue if MK supported the 1-4MB RAM extension. MK3 on the Playstation was a launch exclusive if I remember correctly. It was still on the 16bit machines, but Sony had a deal to make it exclusive at launch. It was pretty close to arcade perfect, except for the loading.
The 32x version is an enhanced version of the Sega Genesis game overall. The sprites are the same resolution, but higher colour than the Genesis/ MD originals. The 32X adds a high colour menu, high colour sprites and BG objects to the game. But it still relies on the Genesis for the BG layers. Uses the Sega Genesis colour palette. Which leaves some mismatched results with 15 colour BG layers and 134 colour 32X sprite layers.
The SNES does have a higher colour output in comparison to the Genesis game, the sprites are lower in horizontal resolution than then Genesis/ MD counterparts. The SNES sprites were done this way to accommodate the SNES's lower horizontal resolution output. When the framebuffer outputs to 4:3. the sprites do look comparable in size. In MK1 the SNES sprites would look extra wide. The SNES has a really good port of MK2. MK3 on the Genesis has higher resolution sprites as well in comparison to the SNES port.