As ShadowCraft has now been updated, there are fewer known issues. Alas, "fewer" does not yet mean "none". I will try to keep track of known issues here. For the moment asking about issues found herein will be a 1 point infraction; however, I reserve the right to increase that number if people don't seem to be getting the message.
1. LFR Wrath of Unchaining is still buggy. I'm not entirely sure why.
2. The legendary questline daggers do not rank properly in the item dropdowns. They score correctly once equipped, just not in the items ranking. This is unlikely to be fixed.
3. The 2pc T13 is somewhat underestimated in quality.
4. The legendary proc is currently being modeled as purely a stacking Agility effect rather than a resetting stacking buff with free finishers mixed in. This probably slightly underestimates its damage contribution, and likely skews EP values - particularly ones that modify finisher damage, i.e. Mastery for Assassination and Subtlety - to some extent.