Both possibilities could be true. In order to distinguish them you should run a time course: 1. If you see an early increase in Anexin+/PI- followed by an increase in Anexin+/PI+ you might have apoptosis. 2. In contrast, if you see a direct increase in Anexin+/PI+ without Anexin+/PI- you might have necrosis. However, you will need to confirm using inhibitors of caspases or necrostatin.
Early apoptotic cells are stained by Annexin V but not PI because plasmic membrane is intact while externalizing AnnexinV. Late apoptotic and necrotic cells are stained by both PI and Annexin V. If you want to distinguish late apoptotic cells from necrotic ones you have to stain them with a Tunnel assay that stained DNA fragmentation a late apoptotic event.
Souce: NovoPro 2018-05-07