YAML's indentation rules are easy to break, and many APIs only accept JSON. TOML is unambiguous and pleasant to edit by hand. YAML is at home in configuration files written by people; TOML is the usual choice for simple configuration files.
Keys, nesting and values carry over. Comments in the YAML file are not carried over, because only the data is read. A YAML file with several documents (separated by ---) is read as a list of documents. TOML needs named keys at the top level and cannot store empty (null) values, so a file with a top-level list or a null is refused, with the offending key named.