Tokyo Ghoul Ending, Explained
The manga ends in survival: six years on, Kaneki and Touka have a daughter. The anime reached that ending in :re only by setting aside Root A, which had left Hide mortally wounded.
Spoilers throughout. This page assumes you have finished the series.
Which ending you get depends on what you watched, and unlike most cases of that the anime did not simply tell the story differently. It removed a piece the ending needed and then had to put it back.
The manga ending
After the Dragon crisis, the story jumps forward to an epilogue six years after Kaneki defeats Furuta. Kaneki is alive, settled, and has a daughter, Ichika, with Touka.
Where the anime came apart
Root A, the second season, was billed as a different Tokyo Ghoul, but what aired was, in Anime News Network reviewer Jairus Taylor's words, "something more akin to a condensed version of the existing back half of the first manga, with a few tweaks and anime original scenes." Its most consequential change is Hide's fate in the raid on Anteiku: mortally wounded, he dies, and the final episode follows Kaneki walking into the enemy's camp with Hide's body in his arms.
In the manga Hide is reported missing after speaking to Kaneki, and much later in the sequel he returns, misidentified by the CCG as a ghoul known as Scarecrow, and apparently part of a group trying to retake the CCG from Furuta. The anime had written off a character the ending depends on.
The consequence arrives exactly as you would expect. When the adaptation reaches :re and needs him, Hide is simply back: :re follows the manga's continuity and does not reconcile most of Root A's anime-original plotlines. The anime is not being unfaithful at that point; it is being faithful to a story its previous season had contradicted.
Why this keeps happening
An anime that overtakes or rewrites its source is making a bet about what the ending will need, and the bet is usually placed by people who do not know yet. Writing a supporting character out early is cheap drama with a delayed invoice.
The Promised Neverland broke its ending by shrinking a cost, and this one broke its ending by writing out a person. Compare both with Fullmetal Alchemist's 2003 series, which departed from its manga deliberately, committed to it, and built a conclusion that works on its own terms. The difference is not fidelity. It is whether anyone decided.