I have figure out the bug and a fix will be int he next update. The quick fix is to make sure you are not using all 5 basic firepower modules when going up against a boss. Unfortunately, this means that you will be a weapon short, but the bug will give you an extra basic firepower module afterwards so you can have all 6 against normal enemies.
Sorry for this bug. I know how frustrating it must be to come so far only for the game to freeze. An update should be released within the next couple of hours with some much needed bug fixes and changes.
Thanks for the report!