ending (Spoiler)

Following the timeline of events during Tonia's imprisonment,(confirmed in Bugajski's notes) she got out in the spring of 1956, which ended the Stalinist period/terror in Poland with the release and rehabilitation of all political prisoners. The official, historical date is June 1956.

People could and did re-unite with their families/children regardless of their "crimes" against the system. They tried to pick up the pieces, if possible. Tonia was lucky to be informed where her child was placed.

Same happened to my uncle. He led a Home Army (AK) partisan unit in southeastern Poland, got arrested after the war, interrogated, tortured and ultimately sentenced to death. Later, after many appeals and help of a well-connected lawyer, they changed his sentence to life and in 1953, after Stalin's death, to 25 years in prison. He got out in 1956 after 9 years in various prisons and resumed his terribly fractured life(first by the WWII and then the Stalinist regime)by re-uniting with his family.

You're trying to apply current legal standards to the post-war, Stalinist Poland reality. With 6 mln people dead after the war, the country became one, big orphanage. Due to chaos and enormous devastation, there was no adoption/custody process like you imagine. Warsaw was leveled to the ground and for years people lived in communal apartments, divorced or married, families and strangers, just like you saw at the beginning of the movie. Tonia and Kostek lived in such a communal apartment with other friends.

Malgosia doesn't live with her "dad". He only visits her at the orphanage to take her out so he must have brought her to their apartment. With his last name same as the girl's mother the orphanage had no idea. Or, since the girl was placed there by the government security apparatus, it's possible the Lieutenant instructed them that the girl has a father that might be seeing her. This is not some private institution but a state run place.

It seems that before the Lieutenant decided to kill himself he notified Tonia's ex-husband about the child. He might have told him the whole truth or not. He was the one who deliberately destroyed Tonia's marriage but once he realized there's no future for him and Tonia, his conscience, paternal feelings and love for Tonia made him attempt to reconcile the situation. Also, since the stalinist system was collapsing and the ideals he so believed in were being repudiated, he felt disillusioned and betrayed.

Tonia and Kostek may not ever reconcile but the poor child is innocent in this horrific situation so apparently Kostek decided to be the father at least till Tonia gets out of prison. Maybe he forgave Tonia but in the last scene the child is knocking on the door, calling daddy but there's no answer, just silence.

You're thinking in terms that do not apply to these times. The movie shows you how 'law' worked so don't be surprised by the ending. In a time and place ruled above any laws, no such terms as 'illegitimate' or 'custody' had any revenue. Consequently there were no standards of operation.
That's it for facts, so try to see the last scene more symbolic. It's all there in her face, a mix of emotions - hope, fear and mostly not knowing what's behind the door, as we, the viewers don't know.

Never go to bed angry, stay awake and plot your revenge.