First of all, welcome to de Nederland!
Next time, you try to express that you just arrived and your Dutch is not sufficient that you're not sure what status was of your check in. They usually are kind people and use common sense in such questions. Don't afraid about people in uniform here, they are much less burocratic than in our home lands.
About the questions:
- I don't think that such small crime (if it would be crime) can trigger permit revoking. I was not able to find online circumstances for this case. So if you worried just call IND.
- I don't remember any yellow message while checking. Here is educational video about using ov with NS. Here is also information what to do if you forgot to chek in/out
Pay attention that on some stations GVB (Amsterdam Amstel) checkin points are together with ns, so you might checkin/checkout wrongly. Also on some NS stations are red check in points to pick up special ticket for fast train between Amsterdam and Breda (Schiphol, Rotterdam, Breda).
Small correction: GVB is the transport provider in the Amsterdam and NS is the trains provider.