That definitely sounds like it could have been the issue. Have you read this support page from before?
Every time the particle passes a boundary it would count as an interaction, so if you have a lot of boundaries stacked your reasoning makes sense that you would reach the max number of interactions (1 million) faster as it is passing 2 boundaries every time it changing cells. For the future I would just make sure you’re using the same surface for coinciding cells as this would prevent this issue, as well as general particle loss issues you might experience in more complicated geometries as the cells don’t align.