It is possible to select two primary powers in one beacon, and it will give both of these powers (at level I). Doesn't seem like this is intended behaviour, because the GUI still shows only one power being selected even though two powers are active.

How to reproduce

1. Build a 4-layer beacon. Get an ingot/gem. Open beacon's GUI.
2. Select any primary power on the left.
3. Select level II of that power on the right. So far everything is normal.
4. Select any other primary power on the left. The first power you chose a moment ago is no longer selected in GUI, so it shouldn't activate.
5. Place an ingot/gem inside of the beacon.
6. Hit the "confirm" button.
7. Both powers are being activated at level I.