In the kanji lesson (the pink item) you are taught just one reading. For 山, you learn the onyomi, which is さん.
In the vocab lesson (the purple item) you are taught the reading for when the item appears as a word. For 山, it is read やま, the kunyomi, when it is a word in a sentence.
For instance, これは山です is これはやまです.
But the onyomi will appear in compounds. For instance, ふじ山 (Mount Fuji)
So, これはふじ山です would be これはふじさんです.
You’ll get the hang of it as you go.