Something to keep in mind is that sometimes a pool will be paid directly to include a transaction with a small fee.  So, while it may appear that it would have been beneficial to include some other transaction, that's only because you are unaware of that separate payment that was made directly to the pool.

Additionally, some pools may choose to reserve a small percentage of the available block space for extremely small fee transactions, as a charitable service to the community.  I'm pretty sure that viaBTC provides a limited number of requests per hour for very small fee transactions to be included in their next block.