If a beacon you've installed appears on the wrong floor, the most common reason is insufficient number of observations of the beacon in the fingerprint data "on the floor plan" where it was installed.
Two possible fixes:
a) Fingerprint more near the beacon on the same floor.
b) Use Beacon Planner (see details below).
Setting beacon locations and IDs with Beacon Planner is most valuable when:
1. If the deployed floor areas are small, using the Beacon Planner may improve first fix accuracy in edge areas, like near walls.
2. If fingerprinting didn't capture all beacons due to, for example, a suboptimal phone being used or too low beacon power, plus the site is perhaps far away. In such a case beacon power can be increased after fingerprinting and Beacon Planner can be used to include all intended beacons in the maps.
3. If beacons are replaced, the new beacon IDs can be imported using Beacon Planner to avoid the need to re-fingerprint.
4. If the fingerprinted area of a floor is very small compared to the floors above/below, some beacons may end up on the wrong floor level. Here, Beacon Planner can fix the problem beacon's floor level.