This is an interesting question, and one which Faustus ponders himself—what does this “portend”? It can be interpreted as a last intervention from God, warning Faustus about what he is about to do. Obviously, Faustus cannot willingly make his blood congeal in his veins. He is sure that his soul is his own and that he should have jurisdiction over both it and his body, but in this moment, Faustus is given a warning that this may not be entirely true—God can still intervene and hold Faustus back, asking the question as to whether Faustus can really claim full dominion over this immortal aspect of himself. However, God does not press the matter—Faustus has his free will. Having been warned, for the last time, Faustus is then left to his own devices, to accept devilish remedies and set his blood flowing again to sign.

"My blood congeals and I can write no more".

 Thus speaks Faustus, on trying to sign his contract with the devil, which Mephistopheles has told him already, has to be signed in blood. The second time, Mephistopheles brings fire to dissolve the blood and allow him to sign, but not before Faustus has considered the congealed blood as an ominous sign:

What might the staying of my blood portend?
Is it unwilling I should write this bill?
Why streams it not that I may write afresh?
Faustus gives to thee his soul.
Ah, there it stay`d. Why should`st thou not?
Is not thy soul thine own? Then write again.
Faustus gives to thee his soul.

Is it a scary moment designed to warn Faustus at the last moment before it's too late? Who knows what to think of it - but it's a significant moment in the play: it marks the last chance Faustus has to go back on the deal.