Perosnally, I struggle the most with backgrounds and making them look nice. I drew an apartment and forgot to put windows in the living room. The layout of the main character's house also makes no sense and is also missing windows....which I didn't notice until later. Oops.
Something that I see some newbies struggle with is the concept of visual storytelling. Like having varied composition (beyond medium shots of characters plastered in the middle), having characters emote with their dialogue, and having the narrative flow.