There is really no sign here of any 'discrepancy' at all. In the quoted/translated passage from 'De Revolutionibus', Copernicus is pointing out that the apogee of Mars' orbit has shifted between the time of the observation reported by Ptolemy and his own time. The quoted passage then goes on to refer to Copernicus' theoretical mechanistic ideas for the celestial motions, which explain this motion as well.
Insofar as these ideas and mechanisms involved circles and epicycles, they have become obsolete since Copernicus' time, but that is of course different from any matter of discrepancy. 'Discrepancy' normally implies some kind of incompatibility or contradiction. But the slow motions of apogees over time contradict nothing: planetary tables from Ptolemy's day to the present acknowledge and incorporate such motions. They are part of the natural order, not any sort of discrepancy or mistake.
It may help any further discussion to quote a somewhat better English translation of the passage in question (i.e. not subject to the hazards of machine translation). This is from Edward Rosen, "Nicholas Copernicus on the Revolutions. Translation and commentary", (Polish Scientific Publishers, Warsaw/Cracow; also Macmillan; also Johns Hopkins, Baltimore; 1978). The reference to an apogee is to the apogee of Mars' orbit ('eccentric') around the sun:-
... computed backwards, the place of the eccentric's apogee in this
last observation obviously = 119°40' [ = 133°20'- 13°40'] in the
sphere of the fixed stars. In Antoninus [Pius'] time Ptolemy found the
apogee at 108°50' [Syntaxis, X, 7 : 25°30' within the Crab = 115°30'-
6°40']. It has therefore shifted eastward 10°50' [= 119°40'- 108°50'
from that time] to ours. I have also found the distance between the
centers smaIler by 40P [1460P as compared with 1500P] whereof the
eccentric's radius = 10,000P. The reason is not that Ptolemy or I made
an error, but that, as is clearly proved, the center of the earth's
grand circle has approached the center of Mars' orbit, with the sun
meanwhile remaining stationary. For, these conclusions are mutuaIly
consistent to a high degree, as will become plainer than daylight
hereafter [V, 19].
Clearly, in the final sentence included here, in the quotation from the Rosen translation (omitted by the questioner), Copernicus was saying that everything is consistent, and at the end of the later chapter (V, 19) to which he refers, he concludes:--
Thus also in the case of Mars the sizes and distances of its motion
have been explained through sound computation by means of the earth's