The irony of reality
The relationship between reality and perception is not simple. It has been as the center of philosophical discussions as far back as Plato, and Alan affirms some of what was first said by Plato, mainly that there are essentially two realms, the present, material reality, and some other form of reality that we don't sense or perceive easily. The idea that there is more to reality than meets the eye is ironic.
The irony of knowledge and faith
The central idea of the Anticlaudianus has to do with the application of knowledge. The ironic part is that for the spiritually significant aspects of life, Alan believed one must practice religious faith, instead of reason. In other words, the ideas that would help give us a sense of purpose in life, those must be determined in a way that is not primarily reason-based. Our best tool for understanding the world doesn't help us understand ourselves or our relationship to the universe, except by way of science.
The irony of simplicity and complexity
One might expect an issue to be more knowable the less complex it is, but actually, the picture Alan paints is a little different. The more essential or central an issue is to the meaning of life, the more difficult it will be to rationalize it, and for the truly central issues of life, reason doesn't seem fitted to help much. The most simply, fundamental things are the things we can't quite wrap our heads around.
The irony of Platonism and mysticism
Plato has long been understood as the first Western thinker, and many of his ideas still shape our Western philosophy of the world, but actually, Alan shows a type of Platonism akin to mysticism, and so he highlights the irony between Greek philosophy and religious mysticism. Ironically, even though the aims of Greek philosophy are rational instead of religious, the fundamental principles of Neoplatonism are mystic—that the world is both knowable and unknowable (order vs chaos), that the mind is trustworthy, but limited in scope, and that the spirit should use another faculty for religious life instead of reason—these ideas are also shared by religious mystics, even though they're the product of logical means.
The irony of science and religion
A modern person is more likely to believe that science and religion are contradictory, but actually, the origins of the scientific process have their roots in religious reasoning, especially thinkers like Alan of Lille who helped herald the cause of observation and logic, but he did that within the context of Medieval University, which was a religious institution.