Just chipping in with a few points in no special order of importance/severity.
1.
Irregular work hours resulting in abnormal sleep patterns which in turn leads to less and worse quality of sleep. Series of early starts, late endings or even all nighters. Even worse when in combination with a normal family life. Can be mitigated quite a lot with good rostering (fatigue management).
2.
Dry air (3% humidity in your average airliner). Resulting in dehydration, dry eyes, dry skin etc.
3.
Sitting for long periods. Can result in tight hips/hip flexors, rolled shoulders and a host of others negative effects. No option for a standing desk in this office.
4.
Radiation. More in higher altitudes and latitudes (ie. polar)
5.
Noise in the cockpit (different between acft types, newer jets generally quiet)
6.
Irregular meal times. Usually eaten off a tray on your lap.