How to indent a code chunk without adding a list

I don't really understand what do you mean by this.

If I use the following, where I've used no lists, I obtain reprex.pdf (119.5 KB). As you can see, the code chunk is identified correctly.

title: "Example"
output: pdf_document

# first heading
some text

# second heading
will include some code now

```{r }
y <- rnorm(n = 100)
plot(x = y)

text after code

# third heading
again some text

Will you please share a small Rmarkdown code to illustrate your problem in form of a reprex?