Specific to the health of the baby, no, you should not have any concerns over a single flight, or even over an occasional flight. From the American Congress of Obstetricians and Gynecologists is this helpful guide to air travel during pregnancy, where they specifically discuss a few risks which I will summarize below. All of this assumes a healthy pregnancy, and before term.
The abstract summarizes it well:
In the absence of obstetric or medical complications, pregnant women can observe the same precautions for air travel as the general population and can fly safely. Pregnant women should be instructed to continuously use their seat belts while seated, as should all air travelers. Pregnant air travelers may take precautions to ease in-flight discomfort and, although no hard evidence exists, preventive measures can be used to minimize risks of venous thrombosis. For most air travelers, the risks to the fetus from exposure to cosmic radiation are negligible. For pregnant aircrew members and other frequent flyers, this exposure may be higher. Information is available from the FAA to estimate this exposure.
My summary of the specific risks from the longer paper:
The pressurized environment of the aircraft can lead to some changes in the mother's blood pressure and heart rate; there is currently no evidence this is likely to cause an issue with a developing fetus, but you can take preventative measures such as wearing support stockings, walking around periodically, and drinking sufficient water.
Turbulence can cause the expectant mother to fall and be injured (which could in theory do harm to the fetus), so when possible sit down with your seatbelt fastened.
Cosmic radiation, etc.
An occasional flight will not cause you to receive more ionizing radiation than the generally accepted safe level; however, many flights could put you at risk of surpassing that level. The specifics, and a link to determine her specific exposure:
Available information suggests that noise, vibration, and cosmic radiation present a negligible risk for the occasional pregnant air traveler (6, 7). Both the National Council on Radiation Protection and Measurements and the International Commission on Radiological Protection recommend a maximum annual radiation exposure limit of 1 millisievert (mSv) (100 rem) for members of the general public and 1 mSv over the course of a 40-week pregnancy (7). Even the longest available intercontinental flights will expose passengers to no more than 15% of this limit (7); therefore, it is unlikely that the occasional traveler will exceed current exposure limits during pregnancy. However, aircrew or frequent flyers may exceed these limits. The Federal Aviation Administration and the International Commission on Radiological Protection consider aircrew to be occupationally exposed to ionizing radiation and recommend that they be informed about radiation exposure and health risks (8, 9). A tool to estimate an individual exposure to cosmic radiation from a specific flight is available from the Federal Aviation Administration on its web site (http://jag.cami.jccbi.gov/cariprofile.asp).
So - no, your partner did not put the fetus at particular risk by flying while pregnant; however, if she is likely to fly many times during the pregnancy (such as, if she works in sales and flies on a weekly basis), she should talk to her obstetrician and ask them whether the particular flight frequency and duration is safe throughout the pregnancy.