Is there a way to look back at the stages to make sure I got all the cards once in the bonus? I know you can get them from ghq but I just can't remember if I got them all.

Check the wiki, if you have all GHQ cards then you missed nothing.

There are 2 Cards in GHQ that cant be obtained at stages.
There are some Cards from stages that cant be obtaned from GHQ.
If you use Bonus stage, N-Gacha and GHQ ypu should be albe to get all Cards from stages as they are now.

For a short time stages gave 2 Cards that player cant obtained anymore - I bug fix changed the cards some stages give.