Is it bad practice to place a LiPoly battery underneath a PCB in an electronic device?
This is standard practice, but, as with anything, you have to consider your specific design.

Here are some possible problems:


If you have anything sharp underneath your PCB, such as through-hole component leads, these can puncture the battery.
The battery may interfere with any RF (or other high-speed) features on your board. Similar to putting the PCB against a metal enclosure.
Similarly, it will certainly interfere with the radiation patterns of any antennas on your PCB which are occluded by the battery.
If the PCB has heat-sensitive components a charging battery may effect them.
Conversely, if the PCB will get hot on its own, this could cause issues with the battery. Many battery chargers use temperature feedback. Also, a battery can fail if it gets too hot.