If you have a working interest in a well, you not only have to pay your share of the drilling and completion costs, but also your share of the monthly operating costs, repairs and maintenance. Yes, in general you are responsible for all costs, regardless of whether they were on the AFE. You will also pay your share of the abandonment costs when that comes around.
I don’t understand the second part of your question. You say the AFE had an estimated $25k for surface damages, but they only incurred $5k. How is that overspending the AFE?