I don't think it's settled that the damage was a bullet hole nor that it was new. It's entirely possible it's been there the whole time and Mike just never noticed it. Or hell, maybe he did notice it and just didn't challenge her because we can tell he's decided to ride it out and see what her game is. Someone should go back though last season and see if there are any scenes where we see that corner of the house. Also, from the bad look we got, I didn't even think it looked like a bullet hole, but if it was, it would have to have come from about where they were standing.The new bullet hole that showed up over the night he was staking out her place came shortly after he handed her an envelope full of cash. I think she might be looking for more than some cash, and I think mike understands that.
What else could she be wanting from mike than cash? Does she want the D? I think she's just going crazy, and I think that's what Mike thinks too.