The words consummatum est are also ironic because in the Vulgate Latin text of the Gospel of John (19:30), these are the last words that Jesus speaks before he dies on the cross:
cum ergo accepisset Iesus acetum dixit consummatum est et inclinato capite tradidit spiritum.
"When, therefore, Jesus had received the wine, he said, 'It is finished' and with his head bowed he gave up the spirit."
Given the fact that Faustus has now sold his soul to the Devil, it is ironic that he should use the final words that Jesus speaks in John's gospel.
As for homo, fuge, stolperia has already given a solid explanation of these words. I would add, however, that the phrase homo, fuge may be an echo of the apostle Paul's letter to Timothy (1 Tim 6:11), where Paul gives the following warning to Timothy:
"But you, man [homo] of God, flee [fuge] from all this, and pursue righteousness, godliness, faith, love, endurance and gentleness." (NIV translation)
Once again, there is at least some degree of irony here. The more learned members of Marlowe's audience may have heard the echo of Paul's advice to Timothy, advice which we may assume Timothy took, but that Faustus will clearly ignore.