It's time for… The War Grok Plot Holes! As I'm getting myself prepared for making a whole ACiT cutscenes fandub, I began to notice a lot of plot holes and inconsistencies in a story claimed to be the best one in the entire R&C history by some people. And maybe that's because I started to watch too much Nostalgia Critic.
Time cannot be changed… Unless our main protagonist is dead, or you're using a time portal
Even though it's not a plot hole… what? Through the whole game they repeat us that "time cannot be changed", "past stays where it is", blah, blah, blah… But when Ratchet dies it turns out you CAN use the clock, as long as you don't "risk any more than six minutes". No. Just no. One of the game's messages (about dealing with the past) is suddenly screwed up. If you cannot change time, THEN YOU FREAKIN' CAN'T! No matter if you travel ten years, six minutes or one second back. And the time portals, that apparently can take you even 10 years back and somehow that doesn't rip the space time continuum. Why didn't they open a time portal too Fastoon? Oh, that would cause more paradoxes… That's just cheap.
"Another Lombax?"
Ok, I can pass Angela, overall the Future saga is a sort of "new story", it doesn't really connect with the original series that much… But Alister? No, just no. They keep telling us that Ratchet is the last Lombax in ToD, but now, it turns out there's a second Lombax. Was he hiding so well? No, he wasn't! So many people knew that he was an exile… Heck, they knew exactly where he was hiding! Why didn't Tachyon deal with him? Was Azimuth so safe in his hideout? NO, HE WASN'T! He was living on a junkyard planet! Even if Tachyon didn't control it… What stopped him and his Lombax obsession from coming there?
Cautious Orvus
Did Orvus predict that he'll be gone before Clank finds himself in the Clock? I mean… he recorded so many messages for Clank, yet there was no real danger of his passing. On a second note, he agreed to talk about the Clock with an outsider… So, he's cautious enough to make all these holo-recordings, but decides to trust someone calling himself Nefarious… Ingenious I guess.
Screwing around with dead
Ok, I can accept the fact that storyteller makes us think that a character is dead, and then suddenly it turns out he's not… But give us a good reason. I already said that "time travel" is not really a good one… And so is "teleporting in the last minute" (Nefarious). What a load of bull… shhhhh! And it's not just A4O - they already hinted that Nefarious survived in ACiT's space radio. I mean… Come on, when did Lawrence come back to teleport him during those 10 seconds?
What plot holes and inconsistencies did you notice?
EDIT
I know you want to do this Darkstar…
If we get enough "story bugs" here, we could make a YouTube video highlighting them 
Also, something else just came to my mind… What happened to Qwark between "Five Bolts Wasted" and final battle? When Ratchet & Clank are shoot into space we see him tied in his Nurse Shannon costume, but then he fights the troops outside the station along with Snowball… How did he break out? Was Snowball waiting there all that time?