This is honestly one of my favorite things to write about. Right now in my novel there are three characters who find themselves with wings they did not have before, and the only one who has figured out flight has also discovered that he had crippling acrophobia resulting from the sheer shift in scale from human to bird. It can even go deeper than that to things that are semi-automatic. One character ran into a problem where she could only breathe properly for the way her lungs worked when unconscious, because otherwise human habits would clash with her biology with dangerous results if she wasn't careful about exerting herself.
The way I see it, reflexes are unconscious things wired into your neurology that would need to be consciously suppressed to stop, such as a body's stress or pleasure responses or involuntary limb movements designed to prevent or escape dangers. Instincts, on the other hand, however automatic they may seem, are still to some degree learned behaviors, often through trial and error in a creature's infancy. Many things people associate with animal behaviors are learned and reinforced through success, and simply wouldn't occur to a foreign consciousness inhabiting a new body unless they spent a significant amount of time in it and made an active effort to learn.
