While trying to console Odo when the researcher who first was assigned to work with Odo falls ill, Sisko speaks about how difficult it was to see his own father get sick and grow frail, and how helpless he felt. Sisko concludes, "But, in the end, I knew there was nothing I could do," suggesting that his father died. However, as we learn later, Sisko's father is very much alive.
Dr. Mora at one point says "Dear God, what have I done?" As a Bajoran, his religion does not contain a God, rather a whole pantheon of prophets. A more accurate phrase would have been "By the Prophets, what have I done?"
Dax has the stone pillar transported from the planet. This is in violation of the prime directive, and safety regulations, since the crew do not know at this point what it is or represents.
The runabout crew all beam down to the planet and leave the ship in orbit. This is a risky manoeuver. They should have left one person aboard to monitor their wellbeing.