Red Squares in RDKit?
In your 3d data some atoms have the same coordinates.

If all coordinates are singular like here

from rdkit.Chem import AllChem as Chem
from rdkit.Chem.Draw import IPythonConsole
from rdkit.Chem import Draw

mb1 ='''
     RDKit          3D

 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.4420   -0.8874   -0.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3758    0.0725   -0.4996 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9154    1.1745    0.2995 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7376   -0.6096    0.1788 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9820    0.2624    0.3084 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0693   -1.6891   -1.4463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8570   -1.3405    0.1088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2571   -0.4005   -1.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1723    1.9659    0.4378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2580    0.8409    1.2857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7617    1.6439   -0.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4357   -0.9719    1.1698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0275   -1.4907   -0.4080 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8280    1.0937    1.0028 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2816    0.6703   -0.6627 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -0.3344    0.6923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  1  6  1  0
  1  7  1  0
  1  8  1  0
  3  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  5 16  1  0
M  END'''


You get a pic without the red box.

mol1 = Chem.MolFromMolBlock(mb1, removeHs=False)
Draw.MolToImage(mol1)




If I give the H on position 15 the coordinates from the C from position 5

mb2 ='''
     RDKit          3D

 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.4420   -0.8874   -0.7989 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3758    0.0725   -0.4996 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9154    1.1745    0.2995 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7376   -0.6096    0.1788 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9820    0.2624    0.3084 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0693   -1.6891   -1.4463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8570   -1.3405    0.1088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2571   -0.4005   -1.3461 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1723    1.9659    0.4378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2580    0.8409    1.2857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7617    1.6439   -0.2155 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4357   -0.9719    1.1698 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0275   -1.4907   -0.4080 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8280    1.0937    1.0028 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9820    0.2624    0.3084 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8161   -0.3344    0.6923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  1  6  1  0
  1  7  1  0
  1  8  1  0
  3  9  1  0
  3 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  0
  5 15  1  0
  5 16  1  0
M  END'''


you get the red box