why is the "yn" missing after the "ddim"
See the course notes for the section 'Wanting'. There is no 'n/yn with eisiau - it is an exceptional pattern.
Isn't same the case with wedi?
Would that be literally "she is not wanting coffee"? In my book "dydy hi ddim" is "she is not"
Literally, yes, but literal translations from one language to another do not always give a good result.
I typed exactly the correct answer. Dydy hi ddim eisiau coffi. But this was marked as incorrect.