This same thing happened to me. Firstly crossed save messed up my account because my primary account is on Xbox. My playstation account which has no characters is now linked across all platforms. As much as I hated it I made another character and had to essentially restart. I can't unlock it for 90 days because I bought silver which is really messed up.
Reluctantly I started again. I grinded out all 6 rivens wishes to craft an apex, I've been playing destiny for a decade now so I've been around. I used the tokens on the apex predators of course and not a single red border was active because I dont own forsaken.
Bungie could have let players know that they won't be able to craft. I simply would have saved it for if I choose to buy. Or just used the wishes on exotics which I desperately need as a new light. This is a slap in the face after spending so time on the game and grinding wishes
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This post is old and actually was fixed a week or so after making it. The issue you seem to be having is that you didn't finish the intro to Witch Queen which unlocks the enclave and crafting. If you don't do that first, any Deepsight weapon you dismantle or extract pattern progress from won't count towards the weapon pattern.
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Thanks bro, I really appreciate your feedback, since I just started I haven't gotten to that yet. You saved me alot of headache and it's good to know the issue had finally been addressed. The witch queen part would be the first thing I do next time I log on.