A compendium is a concise, yet comprehensive compilation of a body of knowledge.
What then would I call an entry or item of knowledge that is contained by a compendium? Is there a general term for what a compendium is made up of?
I think it would depend on what sort of compendium it is.
If it's a compilation of poems, each entry would obviously be a poem. It might be a compendium of books, writings, words, quotations, and any number of things.
The most generic or common term is the one you used: entry. I think for compendiums of knowledge the word article would also be common.