The posted shaped don’t match a binary classification case, as the input seems to have the shape [batch_size=1, nb_classes=1000], while the target has the shape [batch_size=1, nb_classes=2]. Based on the target shape it seems you are working on a multi-label classification. However based on the model output shape it seems you might have forgotten to replace the last linear layer of a pretrained classification model, so that the 1000 ImageNet class logits will be returned.
The error is raised, since nn.BCEWithLogitsLoss expects the model output and target so have the same shape.