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Luther, at the Diet of Worms, offered to show, at any time that might be assigned to him, that councils had erred. He does not seem to have been taken up on this directly, although conversations may have been held in private. About a week later Luther was summoned to see the Archbishop of Treves (Trier), where were assembled several others including Hieronymus Vehus, Chancellor of Baden. The Chancellor began a "long harangue" in which he said that:
the church, like any other power, had its constitutions which might be modified according to the requirements of the particular nations to which they were applied, the diversity of manners, of climate, of epochs; and that herein lay the apparent contradictions which Luther had denounced as existing in the internal system of the church. These contradictions, in fact, only proved more emphatically the religious care with which the church regulated its spiritual administration, and in no degree affected the integrity of the catholic dogma. That dogma was yesterday what it is to-day, and what it will continue to be till the end of time.
Vehus concedes that councils have differed on what today are called "disciplinary" matters, but denies that they have differed on matters of dogma.
Ref: Famous Trials
Luther had previously said, during the Leipzig Disputation of 1519, that Councils contradicted each other and so could not all be certainly correct. It is no necessary to go back far to find an instance of a Council doing exactly that, and in no uncertain terms. The Fifth Lateran Council ran from 1512 to 1517. In 1516 the following was issued at Session 11 (paragraph 15 of December 19th):
Just as pope Leo I, our predecessor of holy memory, whose footsteps we readily follow insofar as we can, gave orders and brought to pass that the measures which had been rashly carried out at the second synod of Ephesus, contrary to justice and the catholic faith, were later revoked at the council of Chalcedon, for the sake of the constancy of the same faith, so we too judge that we cannot, or ought not to, withdraw from or abandon the revocation of so evil a sanction {the Pragmatic Sanction of Bourges} and its contents if we are to preserve our own honour, and that of the church, with a safe conscience. The fact that the sanction and its contents were published at the council of Basel and, at the instance of the same council, were received and recognised by the meeting at Bourges, ought not to influence us since all those happenings after the transfer of the same council of Basel took place — the transfer being made by pope Eugenius IV, our predecessor of happy memory — have remained the deeds of the quasi-council, or rather the conventicle, of Basel,
Here the Fifth Lateran Council is very clearly contradicting the Council of Basel.(1431 - 1445). The Fifth Lateran Council also overturned the Sacrosancta Decree from the Council of Constance in 1415, asserting that Popes were subordinate to Councils. In its second session in 1512 it had condemned the Council of Pisa, 1511, and declared everything it had done null and void.
The Fifth Council is justifying this power to contradict earlier Councils, by the fact that Chalcedon had overturned Second Ephesus more than a thousand years previously.
It is also making the point that some Council are seen, wholly or partly, as lacking legitimacy. In the case of Sacrosancta, it was never approved by a Pope, and so can be, and was, regarded as invalid.
The denunciation by the Fifth Lateran Council, of those earlier councils, was so recent, and so unequivocal, that it must have been clearly in the minds of all involved, as a recent instance of a Council contradicting another Council.
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Martin Luther is referencing contradictions in, amongst other things, the claims of primacy over the church by Rome. This takes shape in various historical attempts. Examples that follow are primacy, purgatory, and filioque. Space won't allow other examples like baptism of heretics, Acts 15 council, primacy of Scripture, and others.
PRIMACY
In Canon VI of Nicea in 325, it appears (there is of course disagreement) that Alexandria, Antioch, and others, like Rome, retained their jurisdictions. In other words, Rome was not given, nor did it claim, primacy over the other Sees.
Let the ancient customs in Egypt, Libya and Pentapolis prevail, that the Bishop of Alexandria have jurisdiction in all these, since the like is customary for the Bishop of Rome also. Likewise in Antioch and the other provinces, let the Churches retain their privileges. http://www.ccel.org/ccel/schaff/npnf214.vii.vi.viii.html
In turn, this jurisdictional issue again unfolded in Canon III of Constantinople in 381, a short 56 years later, in which Constantinople was elevated above the other Sees, yet below Rome (which too was something new). This position of "honor" also met with disagreement over exactly what was meant.
The Bishop of Constantinople, however, shall have the prerogative of honour after the Bishop of Rome; because Constantinople is New Rome. http://www.ccel.org/ccel/schaff/npnf214.ix.viii.iv.html
Here is Luther on the issue of primacy.
He [Augustine] was speaking of only two councils, Nicaea and Constantinople, which he had not seen, but afterwards learned about from writings; and at their time no bishop was over any other. The bishops, neither the bishop of Rome nor any other, could never have brought these councils into existence, if the emperors had not called them together. And so I judge, in my folly, that the great, or universal, councils are so called because the bishops were called together out of all lands by the monarch, the great, chief, or universal, ruler.
For no matter how wild it makes all the papists, history testifies that, if the Emperor Constantine had not called the first Council at Nicaea, Pope Sylvester would have had to leave it uncalled. And what would the poor bishop of Rome have done, for the bishops in Asia and Greece were not subject to him? ... Yet one sees in the histories that the Roman bishops, even before that time, were always seeking after lordship over the other bishops, but could not get it because of the monarch. They wrote many letters, now to Africa, now to Asia, and so on, even before the Nicene Council, saying that nothing was to be ordered publicly without the Roman See. But no one paid any attention to it at the time, and the bishops in Asia, Africa, and Egypt acted as though they did not hear it. http://www.godrules.net/library/luther/NEW1luther_e14.htm
PURGATORY
This council [Nicea] decrees, among other things, that Christians who have fallen are to be received back into penance for a period of seven years; if they die in the meantime, they are to be free, and are not to be denied the Sacrament. This decree the council-criers themselves do not keep, but act against it and consign dying Christians to purgatory with the remainder of their penance. If the pope were to keep this rule, the devil! what a poor beggar he would become, and all the monasteries along with him, if this mine, ore-pit, and trade — viz., purgatory, masses, pilgrimages, foundations, brotherhoods, indulgences, bulls, etc. — were to come to nothing. The devil protect the pope, with all cardinals, bishops, monks and nuns, so that the Church may not be ruled according to this council! http://www.godrules.net/library/luther/NEW1luther_e14.htm
By contradicting the Nicea Council, the Pope of Rome was assigning "fallen" Christians to purgatory from which their ancestors would have to pay to redeem them.
FILIOQUE
The issue with the filioque also sources to canons of Ecumenical Councils contradicting each other. In this case, it is about Canon VII of Ephesus in 431.
When these things had been read, the holy Synod decreed that it is unlawful for any man to bring forward, or to write, or to compose a different (ἑτέραν) Faith as a rival to that established by the holy Fathers assembled with the Holy Ghost in Nicæa. http://www.ccel.org/ccel/schaff/npnf214.x.xvi.x.html
What had happened prior to Ephesus in 381 was at the First Council of Constantinople wherein the phrase "and the Son" was added to the original Nicene Creed of 325. This became the Nicene-Constantinople Creed. Some then subsequently viewed this additional phrase as presumably introducing a different Faith than the one at Nicea in 325. This issue simmered along until boiling over in 1054 with the Great Schism.
GRACE ALONE
Therefore St. Peter fights it and argues against it so hard, and will have men saved entirely by the grace of Jesus Christ alone, without any works.
Not satisfied with that, he was so bold as to say that all their fathers, patriarchs, prophets, and the entire holy Church in Israel had been saved only by the grace of Jesus Christ and nothing else and been condemned only because they had tempted God by wanting to be saved by other means. I think we can call this real preaching, and knocking the bottom out of the cask! Ought not this heretic be burned to death? He forbids all good works and holds that grace and faith are alone sufficient for salvation, and always has been, in the case of all the saints and all the ancestors of all the world. We must needs be called heretics and devils now, because we teach nothing else than this sermon of St. Peter’s and the decree of this council, as all the world now knows better than did the Pharisees whom St. Peter here rebuked. http://www.godrules.net/library/luther/NEW1luther_e14.htm
This doesn't need any explanation.
CONCLUSION
So, when Martin Luther said I do not accept the authority of Popes or Councils because they contradict each other, these are examples.
MORE
http://www.ccel.org/ccel/schaff/npnf214.ix.iv.html
https://en.wikipedia.org/wiki/Filioque