What camera are you using?
There are indeed several possibilities: if you have e.g. an A5100 or A6000 and using continuous AF (AF-C), you see the PDAF points. These are extremely quick AF point (1mm size) located on the sensor to track movement rapidly. The slightly larger green squares are shown if you use AF-S, meaning that it only focusses once and remains locked (on these models) OR that you are using a non-PDAF compatible lens during AF-C.
Then there are green squares around face (face-detection) and double green squares when an object is tracked (called object tracking).
It several items are in the same focal plane, they can all be sharp (if people are standing next to oneother, then can all be sharp). Depending on the subject, you can see one or more green squares on everything the camera believes is sharp.
