Yes, the Chargen menu can cause all kinds of issues for your character. It is not guaranteed to hose, but the big problems that may happen do not show up until you save and reload the character the next time.
Here is what you do, make a forked save first. Load that save, use the menu, make your changes. Then, save the game, new slot or overwrite your forked save, then exit out of the game. Reload the game, reload the save and look at your character's stats. If it is hosed, reload the save from before the menu and try again. Do not try to use the console to fix skills and perks, it will only get worse.