The matters treated by this question imply only partially knowledge of EU law, the rest of insight comes from the sphere of general principles of law. The principle of legality meets the principle of legal certainty in this case.
The principle of liability on the part of a Member State for damage caused to individuals as a result of breaches of Union law for which the State is responsible is inherent in the system of the Treaty. (Köbler para 30 and the cited case law) The obligation of a national Court of last instance (de facto) is to refer the case dealing with matters of EU law for a preliminary ruling (art 267(3) TFEU).
In Byankov we have the case of disregarding the formal requirements, ie the time limits, therefore we have a case where no judicial remedy is available, but no Court ever has adjudicated on the merits. The referring court in case C-249/11 is the one dealing with the matter of reopening the administrative procedure.
Now imagine that another national court confronted with a similar situation has decided not to refer. Would you say that this decision can incur the state liability?
http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=CELEX:62011CJ0249:EN:HTML
http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=CELEX:62001CJ0224:EN:HTML