These can be different pronunciations or different spellings of the same morpheme.
Example
There are three allomorphs of the morpheme -s in English. Compare the sound of the -s in ‘cats', ‘dogs' and ‘foxes'.
In the classroom
Certain allomorphs are difficult for learners to produce correctly, for example the allomorphs of the -ed regular past morpheme, which learners often do not produce correctly until higher levels. Recognition activities such as sorting words into groups according to pronunciation are useful to raise awareness.
Further links:
https://www.teachingenglish.org.uk/article/pronunciation-past-simple-verbs