There was no parliamentary convention preventing Abbott from being called to ask a supplementary question by the Speaker.
While Abbott was not successful in the week's ballot to be placed on the order paper for PMQs - guaranteeing that she would have priority in asking a question - the Speaker may, and in this case, did, call MPs who 'catch the Speaker's eye' and who were not on the order paper. For example, Sir Christopher Chope, Sir Edward Leigh and Mark Francois were all called to ask a supplementary question despite their names not appearing on the order paper.
The Speaker's office released the following statement in explanation:
During Prime Minister's Questions, the Speaker must select MPs from
either side of the House on an alternating basis for fairness.
This takes place within a limited timeframe, with the chair
prioritising Members who are already listed on the Order Paper. This
week – as is often the case – there was not enough time to call all
Members who wanted to ask a question.
This explanation does seem to bear some scrutiny, as no MPs were called from the opposition benches who were not on the order paper. There were eleven opposition MPs on the order paper, and four Conservatives, so to alternate between sides of the Commons only Conservative MPs were chosen to ask supplementary questions.
However, the Speaker could have allowed PMQs to last slightly longer on this occasion to accommodate more questions - as his predecessor John Bercow regularly did.