Per A7.7, an encirclement counter is placed only if the unit is encircled by fire. A7.72 says that a unit is considered encircled if it can't trace a path to the ground but does not call for the placement of an encirclement counter. It sounds like you are placing illegal encirclement counters.
JR
Illegal, if one forgets that the counter was placed to indicate upper level encirclement - which can be annoying if the circumstances of that encirclement are void, which frees the units from the encirclement penalties, whereas encirclement due to fire continues even when the firing units have gone away.
One could imagine that a TPP could provide "Upper level encriclement" counters, which would help enforce the encirclement penalties, but which would remove any ambiguity of the origin of those penalties...