What are the three alleged plot holes?
1. The small one concerning the origin of the Borg, David Mack's scenario includes humans, that being the case I believe humans would be species 2, (or one but most likely two), but in canon humans are species 5618.
2. And I thought this one was pretty obvious, the Caeliar have spent eons looking for species more advanced than themselves in order to evolve. Such species are all around them, the Organian's were pretty close to their system. Then there are the Q, the Prophets and their dark side the Pah-raiths, the Metrons and probably the species that constructed the Guardian of Forever, just to name a few. So in all this time the Caeliar had not found a single advanced race? I actually thought that this might be something Mack would answer in a later novel.
3. We are told that only three Caeliar cities survived the destruction of their planet, we are also told that each of the Caeliar cities were relatively uniform in population numbers. Numbers that were pretty stable because they were practically immortal and produced no offspring.
The City of Axion was thrown back in time to the year 1519, they spent the next 65 years looking for a new planet to settle on. Although they possess the knowledge of warp theory and practical applications all the Caeliar choose to travel at less than faster than light speeds - meaning they didn't travel very far to find a new home. Once they chose a place they began to build shells around the planet and it's sun. We are not told exactly how long this took but we are told when the work was about half way along that it would take another thirty years
The City of Mantilis, was thrown back to 4527 BC, most of it's inhabitants died in the process leaving only a few Caeliar and humans alive. It was from these that the Borg were born.
The City of Kintana, was sent all the way back to another galaxy at the beginning of the Universe, almost 14 billion years. The only view of this Galaxy is seen by Picard and Enterprise.
Enterprise traveled down the subspace tunnel that was formed by Kintana, and at the other end they found a very old galaxy (almost as old as the universe) and every sun in that galaxy was covered by a shell, all the planets, even the stellar dust had all been swept up and used to build those shells.
"The gravimetric disturbances we're reading are from massive number of black holes, including a few that are bigger than any ever seen before...In addition to the singularities, we've detected enough mass to suggest there are billions of very old stars in this galaxy...The reason we can't see them is that they've all been shrouded."
Here is the problem, billions of stars and black holes means at least two billion. We know that a city of the same approximate size took over thirty years just to shroud one planet and one sun. (and a planet is much, much smaller than any sun). But to give a little leeway, lets say it only took 15 years to shroud a sun, given that we have at least 2 billion suns multiplied by 15 years, you still get 30 billion years to shroud all those suns, and the universe is still less than 14 billion years old. The math doesn't work.
So there you are, three plot holes.