Steps to reproduce:

Create a new project with the Universal 2D template
Create a Square sprite (Assets > Create > 2D > Sprites > Square) and drag it into the Scene. In its Sprite Renderer set Color to orange and Order in Layer to 1, drag the GameObject into the Project window to make a prefab, then delete it from the Scene
Create a Tile (Assets > Create > 2D > Tiles > Tile), set its Sprite to the Square sprite and its GameObject field to the prefab
Create a Tilemap (GameObject > 2D Object > Tilemap > Rectangular), open the Tile Palette (Window > 2D > Tile Palette), create a new palette, drag the Tile into it and paint it into 5 separate cells
Save the Scene, then reopen it (File > Open Scene)
Enter Play mode and expand Grid > Tilemap in the Hierarchy, then exit Play mode
Repeat step 6 three more times

Actual results: The Tilemap alternates between having its 5 tile GameObjects and having none:

After the Scene is reopened (step 5): no orange squares are drawn in the Scene view (0 of 5 instantiated)
Play mode session 1: 5 child GameObjects, 5 orange squares
Play mode session 2: no child GameObjects, only the tiles are drawn
Session 3 has them again, session 4 has none, and after exiting Play mode the state of the last session stays

Tilemap.GetInstantiatedObject returns null for every painted cell while they are missing. No error or warning is logged.

Expected results: The Tilemap has one instantiated GameObject per painted cell after the Scene is opened and in every Play mode session.

Reproducible with versions: 6000.7.0a6, 6000.7.0b2, 7000.0.0a7

Not reproducible with versions: 6000.0.82f1, 6000.6.3f1, 6000.7.0a3, 6000.7.0a5

Tested on (OS): Windows 11