Hello. If you want to reference correct numbering for all elements, then you can just do:
#show ref: it => {
// Skip bibliography citations.
if it.element == none { return it }
box(stroke: 1pt + green, outset: (bottom: 1.5pt, rest: .5pt), it)
}
#let bib = ```yaml
cite:
type: article
author: Author
title: Title
```.text
#set heading(numbering: "1.")
#set math.equation(numbering: "(1)")
= Heading <heading>
#figure([], caption: []) <figure>
#figure(table(), caption: []) <table>
$ x $ <equation>
@heading
@figure
@table
@equation
@cite
#bibliography(bytes(bib))
Your code uses heading counter for all elements which is semantically incorrect.