The missing chromosome is the sex chromosome or the one necessary for reproduction. All of the above animals have the appropriate chromosome numbers for positive identity. Horses have left a clear fossil history of their evolution beginning about 55 million years ago in the Western United States. From this group many lines of horses developed in France, including Equus asinus, the ass. The ass family appears to have migrated southward.
Domestic crossing is probably the answer in almost all cases of mule births.
No Female zebras in estrus will willingly mate with any zebra male, but males totally ignore females of another species. Even our own domestic jacks, unless kept away from jennets and mules from weaning and raised with horses, will not mate with mares. Even so, some remain reluctant lovers of mares. Yes, according to some sources. Not very well.