One of the parts has hit the minimum size bound of 0.05 studs and since it can no longer be made smaller, it prevents the rest of the assembly from resizing with it.
Check your building increments, you’re probably resizing it by 1 stud or higher. Make it lower.
Edit: and also the limit is 0.05, so that’s also another possibility too.
You could also import it into blender or any obj converter and create a mesh with different textures which would be just like the model then you could resize the mesh to be smaller (not under 0.05 studs tho)
To do this you need to right click the group of parts then click on export. Then save it to a folder
Then open up blender/obj converter and insert the object into the scene
Then you can create textures/mess with the object
After the object looks good just do File > Export and click the export as obj!
Then just insert the meshpart into your game and you can scale it as far down as 0.05,0.05,0.05! Hope this helped