Placement of numerical references (“[1]”)
The universities with which I am familiar decide at the faculty/school/department level which referencing style will be used in courses that they teach/manage. This means that:   


a standard referencing format is set across all courses and classes within that area
students do not have to struggle with different formats within the same subject
referencing guides with comprehensive examples are readily available for the stipulated referencing format
there is no need to argue/justify/negotiate with variations


If this is not the case, choose a popular referencing format (Vancouver style uses numbered citations) and apply that. Give the students a link to a Vancouver style guide such as this, as well as handing out a printed copy at the beginning of the semester.

When/if they then argue that their referencing is correct it can be compared to the established style guide.

To be truly effective (in changing habits) the referencing needs to be included in the assessment rubric.