A one-to-one relationship should be able to be determined between IDs and elements with IDs. Therefore, controls with duplicate IDs are a failure of the specs of Success Criterion 4.1.1 (Parsing). In XML serialisation, such a document would not be well-formed unless duplicate IDs are explicitly allowed.
HTML_CodeSniffer currently documents this as failure F77. It could be argued that it also fails F17, about not being able to determine a one-to-one relationship between elements - if there were a label or script that referenced the input fields, a one-to-one mapping would not be possible.