The correct spelling of "were short" is /wɜr ʃɔrt/. The "e" in "were" is pronounced with the schwa sound /ə/, while the "o" in "short" is pronounced with the open-mid back rounded vowel /ɔ/. The combination of the "r" and "e" sounds in "were" creates the vowel sound /ɜr/. When pronounced together, /wɜr/ and /ʃɔrt/ form the phrase "were short", meaning something or someone was not of sufficient length or height.
Short is derived from the Old English word scort, which ultimately comes from the Proto-Germanic word *skurtaz. The word were is the past form of the verb be in the second person singular or plural, and it is unrelated to the etymology of the word short.