I frequently (basically every conversation) have issues with Claude getting confused about which version of the file it should be building on. Usually what causes it is asking it do something, then manually editing the file to remove or change something myself and giving it back, telling it it should build on top of what I just gave it. It usually takes three or four tries before it will actually use what I just gave it, and from then on it keeps randomly trying to reintroduce what I deleted.