Stuff like the Barbarian camp on page 10, where half its rules reference another book that currently doesn't exist.
Only being a dozen pages and change into the book, this really jumped out and me and made me wonder how many other fun references and missing rules there will be, and how usable the book will be on its own.
I quite appreciate the future proofing of the book, knowing that when/if I buy the next book the two will be easily compatible.
Strongholds is entirely stand alone atm, as the rules he references can either be safely ignored or easily incorporated into your existing game. He is offering a mechanic for tracking something that is mostly a narrative thing anyway. eg the pirate ship can attack a port city and reduce its development* level. That is easy enough to hand wave as "much of the city was destroyed. The once thriving port if now a ruin filled with destitute beggars sifting through the rubble."
*AFB, this might be civilization level or something like that
The two things that I have a quibble with are:
There seems to be a lot of blank column inches. This is entirely a lay out issue as nothing as missing, but it gives the feeling that the book is not complete. Since Matt has said he is going to update this after some feedback from the players I don't find this too much of an issue - as long as he gets this tidied up after the update.
The other thing is more to do with consistency 5e design philosophy. Someone has mentioned how he uses the "wrong" terminology in some places - its obvious what he means, but it would be nice if he could stick with the current edition terms. He also gives a few cool magic items that ring back to older editions, where the items gives +x all the time and +y in certain situations (attacking opposing alignment). His customised orcs have a "recharge on sort or long rest" abilities that would probably make more sense as a recharge(x) ability like most monsters have.
Otherwise I am very happy with the product, it does exactly what it says on the tin. It gives DMs an easy way to manage some players desire to have a keep/tower/temple without the need for all the players to have one. Balancing some players having a stronghold with others not being interested is as easy as giving the uninterested player a competing magic item. For the most part the book is edition proof, and even game proof. I think this would be easy to implement in any fantasy setting.