What actions of Marilla show that she was troubled in her mind?

The only obvious incident I can see that troubled Marilla was her status as a spinster...... having lost the chance for a husband and family.

From the text:

"John Blythe was a nice boy. We used to be real good friends, he and I. People called him my beau. [...] We had a quarrel. I wouldn’t forgive him when he asked me to. I meant to, after awhile—but I was sulky and angry and I wanted to punish him first. He never came back—the Blythes were all mighty independent. But I always felt—rather sorry. I’ve always kind of wished I’d forgiven him when I had the chance."