It is reasonable to ask whether the Clinton campaign asked Stein to file the complaint and then helped her raise the money to do the recount.* Stein, who the Clinton campaign dismissed and derided (Stein said nasty things about Clinton too) may have been pulled into the fold with the prospect of significant money going to her campaign and party. After the recount the “leftovers” go to Stein and the greens. A nice payday.
It should be noted also that to our knowledge there has never been such a gap between the popular vote and the electoral college as there was in the most recent presidential election. Now, given the weirdness of the election and the new patterns in voting that emerged this may just be another symptom of the general weirdness. However, it may also reflect the fact that in many Dem heavy areas, California, New York, Illinois, states without voter ID laws, there might have been large numbers of invalid votes. If this were true it wouldn’t have changed the electoral college count but it would have influenced the overall popular vote tally.
*Clinton did concede the election.