Troops have been stationed in Chibok since the kidnap but deadly Boko Haram raids continue in the area.
The pope prayed for those who suffer because of violence.
Clashes between jihadists and Fulani herders have intensified in recent months.
Among the irregularities were ‘ballot-box stuffing, multiple voting…and altering of polling station results with the fraudulent addition of extra votes’.
Former president Ian Khama has shaken up the country’s traditionally calm politics by dramatically renouncing his hand-picked successor Mokgweetsi Masisi.