You might want to try this workaround which completed for me!!
[Background - I managed to interact with a shrine in Freeplay before realising it wasn't just a codex entry. I then found the challenge and proceeded to click on the skulls in Fort Tarsis but couldn't find the last one, in the bushes near the pond. I went out into Freeplay anyway and found all the shrines, alas I couldn't interact with the one I already clicked on. So I had 9/10 and couldn't complete the challenge. Bugged!
I thought I'd try swapping to another character and see if completing it on this one would give me the hoods for all my characters. I made the assumption that if store bought items were account bound, and cash was account bound and not character-bound, then maybe these would be too.
I went around Fort Tarsis clicking on all the skulls from scratch, and then went out into Freeplay and went straight to the shrine that was bugged and interacted with it. As soon as I did it completed the challenge 10/10. I then switched back to my main character and checked in the Forge and I was able to see the hood for my interceptor. I haven't checked the other javelin hoods but I assume I have them all, as the challenge is complete on this character too. I'm so relieved I've not missed out on getting them.]
I'd say try this, swap to another character or create a new pilot. Caveat - you will need to complete all quests up to and including 'Incursion' where you go looking for Tassyn's agent, which then opens up the main area of Fort Tarsis with the pool in the middle, so you have access to all the skulls. click on all skulls or just the ones you're missing. Then go out into Freeplay and interact with the shrines or just the ones you're missing, like I did, and voila you might find the challenge has completed. Swap back to your main and check your Forge for new helmets!
Hope this helps!
