What is whole word masking in the recent BERT model?
phil ##am #mon is a subword encoding of the single word “philammon” into 3 tokens. The comment just means that they mask words as opposed to tokens by taking into account subword encoding.

For more on subword encodings take a look at the slides from cs224, especially Byte Pair Encoding, from the Feb 14 subwords lecture at http://web.stanford.edu/class/cs224n/index.html#schedule.