This whole thing with Stein’s bizarre challenge to the results in those three states came was announced to the public much later.I'm sure that the 'whole thing' was actually in progress way before the night of the election. After all, do you think Stein had to wait until all the votes were in to see that she wasn't going to win (assuming that is the premise for her wanting a recount)?
I wouldn't assume it was in progress before Election Day at all. I don't think anyone in the Clinton campaign expected them to lose all three of those states --
especially Wisconsin, where Clinton never even made a single campaign appearance after she was nominated.
They would have had more legal avenues to pursue challenges in these states if they had gotten started on it sooner.