I have conducted a logistic regression in order to identify whether student status (student/non-student), time period (time 1, 2 or 3), or condition (condition 1 or condition 2) predict a binary outcome (buying lunch or purchasing lunch).

I have plotted the predicted probabilities that are saved as a result of the logistic regression to visualise the data. These show a decrease in probability of lunch being bought between time 1 and time 2 for one of the conditions. However, when looking at the percentages of people who bought their lunch (rather than the predicted probabilities), there is an increase between time 1 and time 2.

Is it possible for there to be an increase in terms of percentages but a decrease in terms of probabilities, or does this indicate that something has gone wrong with the model?

I've been told that it could be Simpson's paradox, that it could be that the model is just a very bad fit, or that it means something has gone wrong along the line somewhere, but I don't know what I need to do to test any of these.

Is anyone able to help?