I encountered this issue just now. I had 3 'long' versions, and 4 'short' versions amongst the 7 required for this MOC. All my spare Black and Trans-Clear were short.
Fortunately, I just bought the Hoth AT-ST 75322, and there are 2 Black studs in the set (1 required, 1 spare). I opened the set and they are both 'long'! Perhaps the long version is newer, and replacing the short ones?