As I reread your post, the question I would have asked is not "wht should I have done" but "what should I do".
You said you took her back. So be it. For your relation ship to work you willneed to talk and build trust again. She will need to be open about what happened and why. Apologies may be good, but true understanding is what is important. It is hard to talk about those things and why she left, and why she came back and how you feel about it and how you can rebuild trust, but talk you must.
For you, you have to be brutally honest with yourself and if you feel things are getting better, then stay with it, but if it feels phoney or false or in any way a sham, then it probably is and you should consider parting ways.
Good luck.
jed