This being said, they might have been payed to include transactions, raised the priority of their own transactions or maybe they had to make the choice between broadcasting an empty block or losing the block reward altogether, so i don't know if you can draw conclusions without knowing why they did what they did....
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.
This is really the key to the OP's problem/question.
The "blockchain" fee is neither an upper bound nor a lower bound as to the actual fee that a user will pay. There have been instances in which, due to human error, a person has included a fee that is orders of magnitude higher than the going rate for a similar transaction, and pool that mined the transaction has refunded the tx fee back to the user. Similarly, as is noted above, a pool may receive an off-chain payment for confirming a transaction that is in addition to the "blockchain" fee paid. These off-chain payments may be a subscription-like service, or it could be an ad-hoc like service.