How did you fix it, if you are getting the same error? 
This code shows the issue and the proposed solution:

x = torch.randn(1, 1, 24, 24, 24)
conv = nn.Conv3d(1, 1, kernel_size=(3,3), stride=1, padding=1, bias=False)
out = conv(x) # breaks
conv = nn.Conv3d(1, 1, kernel_size=(3, 3, 3), stride=1, padding=1, bias=False)
out = conv(x) # works