Eye Color in the Conformation Standard by: Yankee Shelties
No they shouldn't be faulted, though judges have been known to exclude a dog from the running based on personal preference rather than going strictly by the standard, which says:
"Eyes medium size with dark, almond-shaped rims, set somewhat obliquely in skull. Color must be dark, with blue or merle eyes permissible in blue merles only. Faults-- Light, round, large or too small. Prominent haws."