In short: 3:89 is an exception (إلا) in 3:86. And 3:90 is not contradictory to 3:89 but rather places an additional condition in it.
An apostate's repentance is accepted - provided that it is sincere and that it happens before his\her death.
كيف يهدي الله قوما كفروا بعد إيمانهم ... إلا الذين تابوا من بعد ذلك وأصلحوا
How shall Allah guide a people who disbelieved after their belief ... Except for those who repent after that and correct themselves.
— Quran 3:86-89
وكفروا بعد إسلامهم ... فإن يتوبوا يك خيرا لهم وإن يتولوا يعذبهم الله عذابا أليما في الدنيا والآخرة
They disbelieved after their Islam ... So if they repent, it is better for them; but if they turn away, Allah will punish them with a painful punishment in this world and the Hereafter.
— Quran 9:74
You are asking about this verse:
إن الذين كفروا بعد إيمانهم ثم ازدادوا كفرا لن تقبل توبتهم وأولئك هم الضالون
Indeed, those who reject the message after their belief and then increase in disbelief - never will their [claimed] repentance be accepted, and they are the ones astray.
— Quran 3:90
"Increase in disbelief" means that they do not repent but rather increase in their enmity and then die as disbeliever, or that they do not repent sincerely but rather are hypocrites, or that they repeatedly accept and apostatize from Islam (4:137), or that their hearts harden and they never get the chance to repent. This is consistent with the previous verse which allows for their repentance and is also consistent with the subsequent verse which says that one who dies on disbelief will not be forgiven. And the same is also conveyed in other verses such as:
ومن يرتدد منكم عن دينه فيمت وهو كافر فأولئك حبطت أعمالهم في الدنيا والآخرة
And whoever of you reverts from his religion [to disbelief] and dies while he is a disbeliever - for those, their deeds have become worthless in this world and the Hereafter
— Quran 2:217