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It is pointed out by FrédéricC in the comments that the reason for this is simply that the quotient is no more a free module, hence the wrong result. Nevertheless, this could return an error message/warning. I have the feeling that this should be done soon as it is in some Todo list on the Sage documentation : https://doc.sagemath.org/html/en/reference/modules/sage/modules/tutorial_free_modules.html