'Come by' means to get/find, but always suggests an element of chance. It means 'manage to acquire', with the assumption that this is not easy or common. It is generally used in phrases like 'Good staff are hard to come by these days'. The implication is that you are lucky if you manage to get hold of good staff. In other contexts, you cannot use 'come by' as a synonym of 'find'. You can't say 'I came by my wallet under the couch', for example. This makes no sense.

To come by, when it means to find, in my opinion suggests a rather fortunate stroke of serendipity. Laurence

Depending on context they can be the same I came by some money on the floor / I found some money on the floor also to come by = to visit They came by my house.