When repositioning a model by using the Align 3D models feature, there is no new version created in the version history as the model is not changed/edited. This is the expected behavior.
If the model is edited/changed in the original authoring software and a new version does not get created after uploading it into Trimble Connect, there may be a problem in the model file. If this is the issue you're facing, could you reach out to the Connect support team (firstname.lastname@example.org)? They can help investigating a possible issue in the specific model file.