The presence of air in a closed jar is of no concern actually, if we assume no air outside.
As a first approximation, let's assume that the Earth has no atmosphere, so as to neglect air resistance. Also, that the jar is small compared to the earth, and it falls for a short distance, so that the gravitational field is essentially uniform, which means that acceleration due to gravity is always in the same direction, i.e., downward, and the magnitude is constant.
Then the falling jar, because every particle of matter is being accelerated at the same rate, behaves like a frame where there is no gravity. This means that anybody inside the jar (or outside, for that matter), which is falling due to gravity only, behaves as if there is no force acting on it. Any particle inside the jar, which was static with respect to the jar at the moment the jar started to fall, will remain static wrt the jar. The effective gravity inside the jar is zero.
About the bee: Flying in zero gravity may not be possible for the bee. Flying is essentially a process that takes place when there is gravity. But if the bee keeps still, it will just remain there and not touch the lid.
Introducing air resistance will slow down the falling of the jar, and there will an effective g-field inside the jar, but I think what you had wanted to know is not about this case.