It's probably not a glitch and i think i may have the answer to the problem, same thing happened to me. As you are panning around the holomap and seeing all the areas marked as "explored" and all the chests and secrets collected i'd be more than willing to bet you're skimming right over an area called "Broken Wing." It's super tiny and easy to miss.
This is the area that connects from "Crash Site" and is accessed by sliding between the semi-closed doors that are located to the left of where you are facing when you splash into the water after sliding down the ice ramp to initially get into "Crash Site" - as if entering from "Imperial Headquarters"
The chest is a heck of a booger to find and what you have to do is drop down in the area with the huge 3 bladed fan that is sticking up from the floor that has one blade broken off. Go through the doorway on that bottom level and make your way through the path with all the stink-bomb type creatures. Eventually you come to a spot where you have to jump up and hang on a red rail to continue forward, but instead of jumping up just keep forward down a small ramp that forced you into some water, then dive and you'll see the chest.
Here's a video somebody already did on finding it, in case it's easier to follow.
Broken Wing Chest Location Zeffo Star Wars Jedi Fallen Order - YouTube
