Spongeblunt: I am having the same issue and found that it has been reported to github 6 days ago, without an answer from packauthor at the time of writing. Someone on github was able to find the issue and version where it was introduced.
"Can confirm this is an issue with all items which are specifically marked with having a stage required. Backdating to previous 'release' version, fixes the issue. Doing further investigation as to which version specifically broke this feature.
Looks like the issue started occurring between versions 188.8.131.52 and 184.108.40.206 (crafting appears to work in 220.127.116.11)" - Kethaias - https://github.com/EmosewaPixel/Modern-Skyblock-3/issues/620
It might be good to keep an eye on the issue there for a workaround.