Why did the Tar-Aiym, if they were able to build a weapons platform capable of affecting other galaxies, feel the need to develop and unleash an uncontrollable plague? Earlier exposition makes it sound like some kind of Resident Evil style lab accident, but seriously, the weapons platform from Flinx Transcendent could have wiped out the Hur'rikku in one or two shots!
The Tar-Aiym were ambitious conquerors in their own right. Possibly they'd wanted to avoid destroying the Hur'rikku-occupied planets altogether, having had designs on that region of space for themselves. By the time they realized the plague had jumped species and was wiping out more than just its target race, it was already too late to burn the border zone's planets as a quarantine measure.
The thranx were fighting the AAnn for generations before they encountered their first humans. Given that they already knew of one vertebrate race that had achieved interstellar travel, their level of astonishment about humans' having done the same seems a bit overstated: would hair vs. scales really seem like a significant difference, in light of all the other similarities between human and AAnn physiology? If someone's already met a talking ant, a talking beetle shouldn't cause as much of a shock, even though ants and beetles differ in many respects.
The events of The End of the Matter are the universe throwing a practice run at Flinx, saving three planets from a black hole using a designed key, a warm-up to saving the universe from the Great Evil using himself, a similarly designed element.
In Mid-Flinx, when she's told that their captors are summoning a shuttle to take Flinx off-planet, Teal searches for a comprehensible translation for "shuttle", and comes up with "skyboat". Why would a Midworld native have the slightest clue what a "boat" is? She's probably never seen a body of standing water bigger than a bromeliad's captured puddle in her life, and even a Midworld bromeliad wouldn't be large enough to need a boat to navigate. If anything, you'd think her people would retain a concept of aircraft — they see flying animals every day — while forgetting watercraft completely.
In the first novel set on Midworld, furcot dialogue is very limited and functional, and Ruumahum seems to see Muf's questions as a time-wasting nuisance. By the second, they're speaking in full sentences and having philosophical discussions of their own, in which Saalahan actively endeavors to teach the two youngsters. This inconsistency could be dismissed in several ways, both in-character (e.g. Born's Ruumahum could've just been very grumpy and terse) and out (e.g. Foster not wanting to reveal how smart furcots are too soon in the first story). But when you consider The Reveal at the end of Midworld about furcots' origins, it's more likely that They-Who-Keep have been getting better at germinating smart furcots over generations, as they assimilate more human remains and improve their own botanical neural network.
There are actually some subtle hints that Abalamahalamatandra is actually a four-part gestalt creature well before The End Of The Matter offers any clear information on what he really is. First, there's how one of his hands slaps another for slapping Flinx when Ab and Flinx first meet. This seems like proof of Ab's insanity, but it could just be a minor disagreement between those two quarter-body segments of him. Also, the one time Ab shows anything approximating real empathy for Flinx, it's right after Pip wanders off with Balthezaar, leaving Flinx alone in his own head for the first time since childhood: a deprivation which Ab, being a fusion of four body-segments' minds, can probably comprehend better than any single-minded creature.