Replacing light fixture

The ground should be connected to the box (usually via a screw). There are screws for that. Light (or whatever) fixture (assuming metal) is assumed grounded when it is fastened to the grounded box. Note that plastic boxes have metal grounding strips connecting the ground wire screw with the threads for the lamp fixture screws so it works the same as a metal box (theoretically).

The new fixture may have plastic or some non-conductive material between where the light bulbs and the fixture base (or the wires are there for extra safety). Are there two lights on the fixture? Might be one for each light source. You can pigtail it to the ground wire or the ground screw on the bracket. All effectively the same..

3 lights on the fixture. Right now the shorter of the 2 ground wires are connected to the green ground screw on the mounting bracket. The other isnt connected and the one that was part of the junction box iant connected to anything either

James Stonehenge wrote: ↑ 3 lights on the fixture. Right now the shorter of the 2 ground wires are connected to the green ground screw on the mounting bracket. The other isnt connected and the one that was part of the junction box iant connected to anything either

The ground wire that feeds into the box along should be connected to the fixture box regardless . Why it wasn’t before is irrelevant, it should have been.
The ground wires from the light itself can be attached to the mounting bracket, the fixture box, or the ground wire feeding the box. It all will serve the same purpose so long as the incoming ground is attached to the fixture box