Just happened to me. I was also on the mission to escape the atmosphere. career mode, hard difficulty, I had the basic command module, with 2 mini red parachutes, 2 large blue parachutes, small storage bay with a goo, thermometer, and pressure thingy inside ,heat shield, decoupler, flea, decoupler, hammer, decoupler, hammer with two flea attached.
I used all my research things and did a crew report around 100,000ft. I didn't get a notification of mission complete, but when I landed I had like 9k research.
Just opened the same game back up after posting the above... I had 100k funds, but was able to upgrade my entire base. I had 94k when I upgraded one of my buildings that said it cost 500k+ but it let me upgrade it and I had 93k left over... definitely broken.