According to Martin Luther, which Councils contradicted each other? At the imperial Diet of Worms, Luther famously said:


  I do not accept the authority of the popes and councils, for they have contradicted each other [...]


What did he mean? Is there a particular pope or Council that he is referring to?
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

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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.